Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

https://doi.org/10.1007/s12088-018-0760-y

REVIEW ARTICLE

Fish Gut Microbiome: Current Approaches and Future

Perspectives
Chandni Talwar1 • Shekhar Nagar1 • Rup Lal1 • Ram Krishan Negi1

Received: 23 July 2018 / Accepted: 17 August 2018 / Published online: 27 August 2018
Ó Association of Microbiologists of India 2018

Abstract In recent years, investigations of microbial flora Introduction

associated with fish gut have deepened our knowledge of
the complex interactions occurring between microbes and Due to their vast ecological adaptations, microorganisms
host fish. The gut microbiome not only reinforces the present enormous diversity, thereby fascinating the
digestive and immune systems in fish but is itself shaped by microbiologists to explore their residence in and on the
several host-associated factors. Unfortunately, in the past, animal bodies. After first insights into diversity of micro-
majority of studies have focused upon the structure of fish bial communities were given by the ‘‘Human Microbiome
gut microbiome providing little knowledge of effects of Project’’, it followed that most of the bacterial symbionts
these factors distinctively and the immense functional and commensals populate the gastro-intestinal (GI) tracts
potential of the gut microbiome. In this review, we have and their interactions among themselves and with the host
highlighted the recently gained insights into the diversity finds great significance to human biology [1]. Since then,
and functions of the fish gut microbiome. We have also intensive research has contributed to an enhanced under-
delved on the current approaches that are being employed standing of gut microbiome for its potential complexity and
to study the fish gut microbiome with an aim to collate all functional contributions only to develop as an attractive
the knowledge gained and make accurate conclusions for area of research among other vertebrates. Representing
their application based perspectives. The literature more than half of the vertebrates with vast ecological
reviewed indicated that the future research should shift diversities and distinctive structural features within their
towards functional microbiomics to improve the maximum intestinal tracts [2, 3], fish has justifiably emerged to be a
sustainable yield in aquaculture. significant class for the examination of the confederation of
microorganisms with their hosts. In the past, the traditional
Keywords Fish
Microbiome
Gut
Metagenomics
culture-dependent methods [4–7] and the use of Denaturing
High-throughput sequencing Gradient Gel Electrophoresis (DGGE) and Temporal
Temperature Gradient Gel Electrophoresis (TTGE) tech-
niques [8, 9] revealed very low fraction of these significant
microorganisms. While these approaches only aimed to
reveal the ‘‘variety’’ constituted in the microbiome, some
early studies also correlated the taxonomic abundance of
fish gut flora with specific host functions [10, 11]. Over the
years, the culture based assessments have led to identifi-
& Rup Lal cation of several probiotic and pathogenic bacterial strains
[email protected]
and still continue being employed in studies of fish gut
& Ram Krishan Negi microbiome [12–14]. In recent years, however, the culture-
[email protected]
independent methods have replaced these traditional tech-
1
Department of Zoology, University of Delhi, Delhi 110007, niques as the direct mining of community DNA hold pro-
India mise to unveil the low abundance and rare taxa [15–19].

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398 Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

While the next generation sequencing (NGS) platforms done to reveal the alpha diversity (within-sample diversity)
have vested ease in deciphering the whole community and beta diversity (diversity among different samples)
structure, they also compel researchers to devise ways to while deciphering the composition of gut microbiome.
mine the complete functional potential of fish gut micro- Most studies corroborate to the domination of bacterial
biome. Further, to test the efficiency and sustainability of sequences in NGS sequencing data from fish gut sources
the beneficial flora is an emerging need. In 2016, the Food with negligible representatives of archaeal and eukaryal
and Agriculture Organisation (FAO) of the United Nations origins [17, 19, 24].
reported that the aquaculture yield worldwide has been To date, the analyses of sequencing data have revealed a
increasing. However, at the same time, about 31.4% of the peculiarly low phylogenetic diversity with Proteobacteria,
commercial wild fish stocks were reported to be fished at Firmicutes and Bacteroidetes representing up to 90% of the
biologically unsustainable levels in 2013. As the demand of fish intestinal microbiota across different species and
fish for human consumption continues to increase, the Fusobacteria, Actinobacteria, and Verrucomicrobia among
aquaculture research must focus on the application of latest the represented phyla [20, 24–31]. This is not very sur-
technologies to improve the maximum sustainable yield prising with our knowledge of the challenges imposed by
(MSY). The gut microbiome is known to play crucial roles the gut environment onto the microorganisms to whittle
in development of fish immune system and aid in optimal down the diversity in the niche. The diversity generally
nutrient absorption [20]. Despite this, the use of NGS increases as the diet of the fish changes from carnivorous to
platforms in studies aimed at exploiting the beneficial flora omnivorous to herbivorous [19]. The composition also
to improve overall fish health lags far behind. Too often, differs due to different environmental conditions. Acine-
these studies only focus on their species specificity and tobacter, Aeromonas, Flavobacterium, Lactococcus, and
effect on fish health while neglecting the change in the Pseudomonas, obligate anaerobes Bacteroides, Clostrid-
overall gut microbiome structure. The microbiome is ium, and Fusobacterium, and members of family Enter-
influenced by a myriad of factors and it is difficult to obacteriaceae dominate the gut of freshwater species [32].
ascertain the individual effects of each of these factors. The guts of marine fish are dominated by Aeromonas, Al-
Tarnecki et al, recently summarized the different factors caligenes, Alteromonas, Carnobacterium, Flavobacterium,
affecting fish gut microbiome while also highlighting the Micrococcus, Moraxella, Pseudomonas and Vibrio [32]. A
potential sources of bias in the results from sample pro- summary of the major bacterial phyla composing the gut
cessing [21]. Apparently, the choice of the study design microbiome as revealed by studies in different species can
also greatly impacts the results. It is therefore important to be referred in review by Llewellyn et al, [33] and much
contemplate at the study design prior to noting the recent studies in Table 1. Abundance of similar bacterial
important inferences. In this review, we aim to summarize phyla irrespective of the taxonomic position or geograph-
the different study designs currently being employed in ical location of the fish indicates a role of microbiome in
order to delineate the influence of the different selective important host functions such as nutrient absorption,
pressures affecting fish gut microbiome. The important digestion and generation of immune response. Further, the
findings from recent metagenomics studies are noted. The structural similarity of fish gut microbiome with that of the
review also discusses the future perspectives of fish gut mammals indicates towards the vertebrate core gut
microbiome research and sheds light on the need to focus microbiotas.
on applied microbiomics.

Functional Potential of Fish Gut Microbiome

Composition of Fish Gut Microbiome
Till date, majority of studies on fish gut microbiome are
The colonization of fish gut starts early in the larval stage restricted to diversity analysis and most of our knowledge
and is continuously driven towards achievement of a comes from its correlation with the necessary host func-
complex assemblage of gut associated microbes [22]. tions (Table 1). In this regard, computational tools have
Approximately 108 bacterial cells belonging to over 500 been developed that may provide important predictions of
different species are reported to populate the fish GI tract, the functional capabilities of the community, once the
which are dominated by aerobes or facultative anaerobes taxonomic composition is deciphered using marker gene
although strict aaerobes have also been detected [7, 23]. based approach e.g. PICRUSt [34] and Tax4Fun [35]. The
While considering a metagenomic sample, the diversity is most widely studied functional attributes of microbiota
defined in terms of number of OTUs. OTUs are number of include digestion and immunity. In grass carp, the ability to
clustered similar sequences ([ 97%) that define a taxo- digest plant matter is long been associated with the higher
nomic unit on the basis of divergence. OTU analyses are abundance of cellulolytic bacteria in the gut of herbivorous

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 Table 1 List of some recent studies concerning fish gut microbiome. In all cases, the targeted region used for amplicon sequencing is the hypervariable region(s) of bacterial 16S rRNA gene
sequence which is denoted by its standard code(s). AU and AL, here, stand for autochthonous and allochthonous microbiomes respectively
Host NGS platform Amplicon/ Microbiome Study design Problem Dominant phyla Important inferences References
shotgun addressed
Sequencing

Silurus meridionalis Illumina Hiseq Amplicon: AU and AL Gut microbiome Effect of host Tenericutes, Fusobacteria, Microbial diversity increases [107]
V4–V5 of lab-reared age and— Proteobacteria, and Bacteroidetes with host age; is significantly
fish over associated Abundance of Tenericutes
developmental factors on gut decrease while Fusobacteria,
stages microbiome Proteobacteria and increase
with host age
Silurus meridionalis Illumina HiSeq Amplicon: AL Gut microbiome Spatial and Fusobacteria, Firmicutes, Distinguishable communities [108]
V4–V5 of stomach and temporal Proteobacteria, and Bacteroidetes between stomach and
intestine at microbial intestine; higher diversity in
different time dynamics stomach.
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

intervals after within gut Firmicutes increase and

feeding Fusobacteria decrease after
feeding
Danio rerio Illumina Miseq Amplicon: Not defined Microbiome of Effect of gluten Proteobacteria, Actinobacteria, Legionellales, Rhizobiaceae, [109]
V4 formulated diet formulated diet Firmicutes and Bacteroidetes and Rhodobacter abundant in
fed group (GFD) on gut dominated control samples. GFD fed group. Cobalamin
compared with microbiome Planctomycetes, Fusobacteria, synthesizing Bacteroides and
that of control and Verrucomicrobia dominated Lactobacillus present in
GFD samples control group and absent in
experimental group
Siganus fuscescens Illumina Miseq Amplicon: AU and AL Microbiome of Differences at Proteobacteria, Cyanobacteria and Midgut communities highly [110]
V4 different the level of Firmicutes diverse for both adherent and
regions in GI individuals, gut non-adherent microbiome;
tract locations and Greater diversity of adherent
sample types microbiome accounting for its
active selection by host
Gambusia affinis Illumina HiSeq Amplicon: AU and AL Effect of broad Microbiome Proteobacteria, Planctomycetaceae; Antibiotic treatment lowers the [111]
V4 range antibiotic composition Myroides genus of Flavobacteria diversity and unstably alters
rifampicin on and its dominated during treatment the composition to become
gut microbiome response antibiotic resistant during
towards treatment while the
antibiotic microbiome takes long to
stress recover
Oncorhynchus mykiss Illumina Miseq Amplicon: AU and AL Juvenile fish fed Role of dietary Proteobacteria, Firmicutes, Gut microbial diversity [72]
V6–V8 with plant- and nutrients Bacteroidetes, Fusobacteria and decreases as the source of
animal-derived source in Actinobacteria nutrient derivation in diet is
dietary proteins microbiome restricted
composition
399

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 Table 1 continued
400

Host NGS platform Amplicon/ Microbiome Study design Problem Dominant phyla Important inferences References
shotgun addressed

123
Sequencing

Carassius auratus Illumina Miseq Amplicon: AU and AL ‘Red-operculum’ Differences in Fusobacteria, Proteobacteria and Distinct differences in [112]
V4–V5 disease affected healthy and Bacteriodetes microbiome composition in
individuals diseased gut two groups; potential of some
compared with microbiome species as disease-specific
healthy bacterial signatures
individuals
Ctenopharyngodon Pyrosequencing Amplicon: AL Species with Relationship Fusobacteria, Proteobacteria, Gut microbiome composition as [71]
idellus, V4 three different among host Bacteroidetes and Firmicutes well as metabolite profiles are
Megalobrama feeding habits evolutionary significantly altered by host
amblycephala, raised under distance, gut species and feeding behaviour
Carassius auratus, identical microbiota and
Hypophthalmichthys husbandry metabolic
molitrix and H. conditions profiles
nobilis,
Danio rerio Illumina Hiseq Amplicon: Not defined Adaptive Ecological Proteobacteria, Fusobacteria and Functional adaptive immunity [113]
V4 immune filtering of Actinobacteria affects the neutral assembly
compromised microbiome processes; Adaptive immunity
individuals composition by specifies the microbiome
compared with adaptive composition in each host
wild-type immunity of which otherwise seems to be
individuals the host much similar; Co-housing
individuals of different
genotypes increases the
microbiome diversity
Salmo salar L. Illumina Miseq Amplicon: AL Lab reared and Effect of habitat Firmicutes, Proteobacteria, Presence of core gut microbial [61]
V3 and commercial on microbiome Tenericutes flora regardless of the habitat
V4 freshwater fish composition type indicating operational
farm host selective forces
Salmo salar Ion Torrent Amplicon: AU and AL Reference and Effect of Firmicutes, Proteobacteria, Significantly different adherent [114]
V1 and experimental alternative Fusobacteria, Bacteroidetes, and non-adherent
V2 groups fed with diets on Actinobacteria communities; Non-adherent
alternative microbiome microbiome much diverse and
protein sources structure and diet-dependent than adherent
function microbiome
Oreochromis niloticus Illumina MiSeq Amplicon: AL Cadmium(Cd)- Toxic effects of Fusobacteria, Proteobacteria, Probiotic supplementation [115]
V4–V5 exposed, Cd- pollutants on Bacteroidetes and Firmicutes improved the gut health status
exposed and microbiome in Cd-exposed fish to prevent
probiotic fed, and application death
only probiotic of probiotics
fed and control for treatment
groups
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414
 Table 1 continued
Host NGS platform Amplicon/ Microbiome Study design Problem Dominant phyla Important inferences References
shotgun addressed
Sequencing

Carassius auratus Illumina Miseq Amplicon: AL Development of Factors Proteobacteria, Fusobacteria and Gut microbial diversity [62]
gibelio V4 microbiota in a governing Firmicutes increases as the fish develop
bacteria-free colonization of and is less affected by
fish gut germ- free gut surrounding environment than
ecosystem over by host diet and development
a year
Oncorhynchus mykiss Illumina MiSeq Amplicon: AL Fish from Complexity of Tenericutes, Firmicutes, Similar gut microbiota [116]
V4 different microbiome Proteobacteria, Spirochaetae regardless of source; shaped
sources i.e. composition in Bacteroidetes by host factors; Differences in
reared in farm differently composition highlight the
and in sourced habitat specific taxa
aquarium individuals of a
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

species
Antarctic Fish spp.: Illumina Miseq Amplicon: AL Analysis of gut Complexity of Proteobacteria, Actinobacteria, Gut microbial communities in [117]
Trematomus V4–V5 microbiota microbiome Firmicutes,Thermi,Bacteriodetes different species are not
bernacchii, composition in and Tenericutes exactly same but also not
Chionodraco hamatus, different different altogether
species
Gymnodraco
acuticeps and
Pagothenia
borchgrevinki
Ictalurus punctatus Illumina MiSeq Amplicon: AU and AL Microbiome at Influence of age Bacteroidetes, Firmicutes, Age has a significant influence [118]
V4 different life as well as the Fusobacteria, and Proteobacteria on the intestinal microbiota;
stages with dynamic Water microbiota strongly
different diet dietary and influence gut microbiota at
formulations to environmental early life stages
study gut factors on gut
microbiota microbiome
across
developmental
ontogeny
Oreochromis niloticus Illumina HiSeq Amplicon: AU and AL Gut microbiome Effect of short- Firmicutes, Actinobacteria and Probiotic administration for a [119]
V4 of cultured fish term probiotic Proteobacteria (control groups) short period significantly
in axenic, administration affects the gut microbiota
probiotic- on gut composition at later stages of
supplemented microbiome life
and later active
life phases
401

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 Table 1 continued
402

Host NGS platform Amplicon/ Microbiome Study design Problem Dominant phyla Important inferences References
shotgun addressed

123
Sequencing

Dicentrarchus labrax Pyrosequencing Amplicon: AU Gut microbiome Correlation Proteobacteria, Bacteroidetes, Gut microbiome is dependent [120]
V3–V4 of two different between gut Actinobacteria and Firmicutes upon the host life history or
nutritionally microbiota genetic background; Different
stressed groups composition, nutritional stresses affect host
and effect on dietary stress microbiome and health
host’s growth and host’s differently
or resistance to health
hypoxia
Ctenopharyngodon Illumina Miseq Amplicon: AL Assembly of gut Effect of Proteobacteria, Firmicutes and Gut environment and other host [44]
idellus, V4 microbiota in ecological Bacteroidetes development processes shape
Siniperca chuatsi, larval and adult processes on the microbiome
Silurus meridionalis, fish gut microbiota
assemby
Carnis megalobramae,
Carassius auratus
Cyprinus carpio and
Canna micropeltes
Danio rerio Illumnina Amplicon: AU and AL Survey of Microbiome Proteobacteria, Firmicutes, Environmental factors more [121]
Hiseq V4 intestinal composition Fusobacteria, Actinobacteria and strongly influence
bacteria at key across Bacteroidetes microbiome at early life
developmental developmental stages
time points stages
Salmo salar Illumina HiSeq Amplicon: AU and AL Influence of Effect of Proteobacteria and others Gut microbiome differs by diet [122]
V6 alternative diet alternative treatment but communities in
on microbiome, feeds on biofilters remain
recirculating microbiome in stable independent of diet;
waters and fish cultured in Gut communities less diverse
biofilters recirculating than those of water and
water systems biofilters
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414
 Table 1 continued
Host NGS platform Amplicon/ Microbiome Study design Problem Dominant phyla Important inferences References
shotgun addressed
Sequencing

Megalobrama Illumina MiSeq Amplicon: AL Influence of Differences in Proteobacteria, Firmicutes, Trophic level strongly influence [19]
amblycephala, V4 trophic level on gut microbiota Fusobacteria, Acidobacteria, the microbiome composition
Ctenopharyngodon the gut in herbivorous, Bacteroidetes, Actinobacteria, of fish from same habitats;
idellus, microbiome carnivorous, Verrucomicrobia and Evidence of a large core gut
omnivorous Cyanobacteria microbiota in multiple species
Siniperca chuatsi, and filter
Culter alburnus, feeding species
Cyprinus carpio,
Carassius auratus,
Hypophthalmichthys
molitrix,
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

H. nobilis
Salmo salar L. Pyrosequencing Amplicon: AL Effect of diet on Diet as a factor Bacteroidetes, Diet, time of sampling and host [123]
V3 to V6 the gut controlling Firmicutes and Proteobacteria specific factors influence the
microbiome microbiome microbes
composition
Oreochromis niloticus Pyrosequencing Amplicon: AU and AL Gut microbiome Impact of rearing Proteobacteria and Actinobacteria Water microbial communities [63]
V1–V2 development in environment strongly shape those in the
larvae on microbiota gut; Correlation between
assembly in water and gut microbial
early life community dynamics
stages
Salmo salar Illumina MiSeq Amplicon: AL Gut microbiomes Effect of Proteobacteria, Firmicutes, Geographical distance has less [124]
V4 of freshwater geographical Bacteriodetes and Actinobacteria impact on gut microbiome;
and marine distance on Diversity and identity of
specimens microbiome microbial communities is
more strongly determined by
life-cycle stage
Pimephales promelas Illumina MiSeq Amplicon: AU and AL Gut microbiome Effect of Proteobacteria, Bacteroidetes and Microbiome is significantly [125]
V3–V4 of triclosan antimicrobial Fusobacteria altered even at low level of
exposed fish compounds on environmental changes but
gut has strong resilience power
microbiome
403

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species [20, 36, 37]. Li et al, showed that gut bacterial exigent for this possession. Ley et al. [46], intricately
community of grass carp is dominated by cellulolytic reviewed the demands imposed on microbial flora by the
Aeromonas, followed by Enterobacter, Enterococcus, GI tract viz. in order to firmly attach to the mucosal
Citrobacter, Bacillus, Raoultella, Klebsiella, Hydrotalea, epithelium of gut wall, microorganisms must possess cell
Pseudomonas, Brevibacillus and that an increase in intake surface molecules for adhesion; the efficient utilization of
of plant-fibre increases the diversity of cellulolytic bacteria all the nutrients calls for the production of an enzyme
[36]. Cellulose degrading bacteria Clostridium, Aero- arsenal; the microbes must also be armed with genetic tools
monas, Cellulomonas and Bacteroides along with other for adapting to the ecological plasticity offered by the GI
nitrogen fixing species are reported to provide assimilable tract and for immunity against bacteriophages. The fittest
carbon in the wood eating fish Panaque nigrolineatus microorganisms that are able to meet the ecological
[38, 39]. Clostridia also dominate the gut microbial flora in demands grow and survive in the GI tract and are able to
different marine herbivorous fish species [40]. In contrast appropriate most niche space to become permanent
to the cellulolytic function of microbiome in herbivorous dwellers, also referred to as ‘‘autochthonous’’. While oth-
species, lipase and protease producing bacteria and trypsin ers, known as ‘‘allochthonous’’ are visitors of the gut that
activity are observed to be much higher in carnivorous derive from the surrounding environment [22]. Thus,
species [19], which further confirms the role of microbiota microbes associate with the host in diverse ways which
in host digestion. In Atlantic salmon fed a plant-based diet, may be simply fortuitous at first and may become obliga-
Lactic acid producing bacteria (LAB) are shown to be tory later. The adherence of the bacteria onto the epithelial
present in higher abundance as compared to those fed with cells is considered an essential factor in determining their
fishmeal-based diets suggesting their potential role in effector functions within host. A link between the biofilm
digestion [41]. Besides digestion, changes in microbiome forming ability of bacteria and successful colonization and
composition resulting from environmental stress results in functions of gut flora is suggested [47, 48]. The ability to
challenged immunity in the host. The gut microbiota pro- form biofilms helps bacteria to survive in hostile environ-
duce important short-chain fatty acids (SCFAs) while ment offered by the GI tract and is seen in cases of both
breakdown of complex sugars which are absorbed in the pathogenic and probiotic bacteria [49, 50]. To unravel the
intestine by simple diffusion or specific receptors and allochthonous communities, fecal samples are generally
confer resistance against pathogenic invaders [42, 43]. examined while mucosal epithelium scraped after rinsing
Therefore, the functional repertoire of gut microbiota are used for analyzing the adherent residents. So far,
appears to be synergic with the host needs. studies on characterization and comparison of the two
community types suggest presumably different composi-
tion and that both serve different purposes within the GI
Fate of Colonizing Members and the Factors tract [51]. High species richness in the digesta (al-
Affecting Fish Gut Microbiome lochthonous) is observed as compared to the mucosa (au-
tochthonous) [52]. This can be understood from the
The gut colonization may either be driven by (1) stochastic knowledge of the exasperating conditions within the GI
or neutral assembly that derives from random dispersal of tract outlined above. Further, there are evidences that the
microorganisms or chance events that land the microbes microbial composition also differs in different regions
into the intestine that are solely responsible for the final along the GI tract, the foregut communities being signifi-
shape of intestinal community; or (2) deterministic or non- cantly different from hindgut communities [53]. However,
neutral model assumes that the assembly is determined by the degree by which these two population types differ is not
the host selective pressures, active dispersal by the host and completely understood and needs further clarification.
host-microbe and microbe–microbe interactions. Studies Interplay of a variety of factors determines the consti-
on zebrafish, Danio rerio, herbivorous Ctenopharyngodon tution of the fish gut microbiome. Quality of surrounding
idellus, carnivorous Chinese perch, Siniperca chuatsi, and water and microbial communities directly influence the gut
catfish Silurus meridionalis over developmental time sug- microbiome of fish [24, 54]. Strong evidences of host
gest that the gut colonization among larvae is governed by genetics, developmental stage, immune status and other
seeding from surrounding environments which then transits host specific pressures on the gut microbiome also persist
to be progressively determined by the non-neutral pro- [33, 45, 53, 55, 56]. In addition, the diet also shapes the gut
cesses as the host matures to become adult [44, 45]. microbiome which displays differential composition with
Therefore, suggesting stochastic towards deterministic difference in dietary intake [38, 57–60]. Hence, the factors
colonization of GI tract. influencing gut microbiome may be broadly grouped into
Though the host GI tract provides for shelter of three classes, which are (1) ecology and environmental
microbes, certain adaptations are demonstrated to be conditions, (2) host specific and (3) trophic level and/or

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Fig. 1 Factors influencing the diversity and function of the gut and extrinsic factors are responsible for either healthy state (normo-
microbiome of fish. The factors may be broadly categorized into biosis) or altered microbiota (dysbiosis) both of which affect the
environmental, diet-associated or host—associated. All these intrinsic growth and development of the fish host

feeding behavior as illustrated in Fig. 1. Each of these gut microbiome. Most approaches rely on the fact that if
factors are discussed in detail in the following section. strongly determined by the environment, the gut micro-
biome must vary among members of a species, both
spatially and temporally, in correlation with the sur-
Study Designs Currently Employed to Study rounding waters and vice versa if strongly shaped by
the Factors Affecting Fish Gut Microbiome host selective pressures. The different approaches that are
currently employed to study the different determining
While some recent attempts highlight both the environ- factors are outlined below.
mental and host associated factors to be significantly
contributing to the microbial composition in gut [61], Microbial Composition and Quality of Surrounding
others suggest a stronger influence of the host selective Waters
pressures [62]. The exact degree with which each of
these factors influence the gut microbiome is not known. Due to being constantly exposed to alterations in water
Clearly, it is difficult to distinguish the host specific and quality resulting from various anthropogenic and natural
environmental effects on fish gut microbiota. The dif- causes, the microbial communities in GI tract of fish should
ference in feeding behavior of different species adds to change repeatedly. Thus, a comparison of the water quality
the problem of investigating the role of each of these and host gut microbiome is expected to improve the
factors. Several different approaches are currently understanding of environmental influence. Shared Opera-
employed to study the degree of their influence on fish tional Taxonomic Units (OTUs) between water and gut

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microflora have suggested the possible role of surrounding peculiarly low diversity presented by the gut microbiome
water in steering of gut microbiota [63]. Salinity of water of different fish species of ecologically and geographically
also largely determines the microbial composition in fish different origins with respect to the bacterial phyla further
gut as revealed from analysis of a large number of species warrants the argument of host selective pressures on the gut
with different ecological needs for survival [24]. Studies on microbiome [19, 23, 26, 27, 69, 70].
wild and lab-reared invasive carp species also establish
environment as a key factor in shaping the gut microbiome Variations at Different Trophic Levels and Feeding
[64]. On the contrary, studies also suggest otherwise that Behavior
the abundant microbial taxa in surrounding waters are not
found in the gut of habitant fish and vice versa suggesting a The microbial diversity in GI tract increases as the diet
much stronger influence of host associated factors than changes from carnivorous to omnivorous to herbivorous
environment [65]. [53]. Cellulose-decomposing bacteria such as Anoxybacil-
Species that are known to survive in different stressed lus, Leuconostoc, Clostridium, Actinomyces, and
habitats are considered apt to assess if a change in Citrobacter populate the gut of herbivorous species such as
quality of surrounding waters other than microbial grass carp, Ctenopharyngodon idellus [20]. On the other
composition also affect the host gut microbiota. For hand, carnivorous species are found to harbor lipase and
instance, the endogenous microbiota in Amazonian tam- protease-producing bacteria such as Halomonas [19].
baqui, Colossoma macropomum that is tolerant to sig- Feeding behavior is also shown to affect the gut micro-
nificant variation in pH levels has been shown to be biome composition in a habitat in closely related but dif-
significantly altered at experimental low pH levels; ferent species. Filter feeding fishes display higher diversity
however, it also displays a strong resilience once pH as they filter large volumes of water and cover large areas
levels are restored [66]. by swimming rapidly [71].

Variations in Different Cohabiting Species Administration of Different Dietary Components

The second approach employs the use of different species The effect of dietary intake on gut flora is not only
inhabiting same water systems. Many studies have revealed restricted to the nutritional composition but also the source
a larger influence of host selective pressures and trophic of nutrients. In general, plant-derived dietary proteins have
level in constraining the gut microbiota than the environ- been linked to significantly reduced diversity of microbial
ment as different cohabiting species are observed to com- flora [28] with an increase in relative abundance of Lac-
prise different microflora in gut. For instance, cohabiting tobacillales, Bacillales and Pseudomonadales [72]. While
species of silver carp, grass carp, bighead carp, and blunt animal-derived proteins nurture Bacteroidales, Clostridi-
snout bream revealed distinct gut microbiome composition ales, Vibrionales, Fusobacteriales and Alteromonadales in
[67] providing for the influence of host specific factors on the gut [72]. A study by Mansfield et al., revealed that fish
the gut micro-organismal communities. Similar results fed with synthetic casein based diet have larger diversity as
were obtained in paddle fish, Polyodon spathala and big- compared to those fed with fish meal or soyabean meal
head carp, Aristichthys nobilis with similar feeding based diet [73]. Effects of a large number of other nutri-
behavior when fed same food and reared in same pond tional components have been reviewed in detail [74].
[68]. Thus host associated factors outplay the influence of
environment. Patterns of Gut Colonization in Gnotobiotic Models

Variations Within a Species at Different The use of gnotobiotic fish models incomparably fit to
Geographical Locations serve the purpose of delineating the processes that fabricate
the gut microbiome structure. Analysis of patterns of col-
Third approach employs studying the microbiome of a onization in germ-free zebrafish GI tract revealed that the
single species found in different geographical locations to host responses may be attributed to specific bacterial
study if it is defined by a core set of microbial communities members of the community [23]. Transplantation experi-
that stably reside in the GI tract due to host-specific ments of gut microbial flora between gnotobiotic zebrafish
selective pressures or if the environment shapes the com- and mouse and between gnotobiotic mouse and zebrafish
munities. In this regard, zebrafish, Danio rario, has been hint towards reconstruction of the microbiome after trans-
extensively studied to establish the strong influence of host plantation to resemble that of conventionally raised fish
associated factors that shape the core gut microbiome of thereby concealing the microbial communities which were
the species [25]. Although differences occur, however, the transplanted in their gut [55].

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Thus, it can be inferred that the microbial composition ingested food may vary among individual hosts and may
of water influences the fish gut microbiome to some extent. comprise of semi-digested particulate matter and bones, the
In addition, diet and genetic variations among individual availability of the starting mass of fecal or gut content
hosts also shape the gut microbiome. To elucidate the exact samples for DNA extraction needs to be taken into con-
degree of influence by each factor would be an interesting sideration while comparing the extraction protocols to
area of study. Even though the microbiome composition of avoid false interpretations. Perceivable differences are
two individuals might differ at the species level, there reported to occur in the purity and concentrations of the
occur significant level of similarity among the microbial extracted DNA employing different methods [88]. Further,
genes that are shared which suggest for a molecular link the purity of extracted DNA does not guarantee a suc-
between the microbial genes and host functions [75]. Thus, cessful amplification and sequencing [88]. Sample prepa-
there is an emerging need for multifaceted analyses to rations pose as a source of variability in testing the
clearly demarcate the host-, environment- and feeding extraction efficiency of a method. Processing the entire GI
behavior derived manifestations of the gut microbiome. It tract along with the luminal content may result in isolation
may be viewed as environment, host specific factors and of a large amount of eukaryotic DNA from fish, therefore,
diet, act in concert to constrain the acquisition of gut diluting the bacterial DNA for sequencing and analysis.
microbiota. The structural composition of microbiota also affects pre-
cise extraction of DNA as the gram-positive bacteria are
more difficult to lyse than gram-negative bacteria due to
Profiling the Fish Gut Microbiome presence of a thick peptidoglycan layer in their cell walls.
This spurs a necessity to ensure complete lysis of all bac-
An illustration of the steps followed to analyze the gut terial cells in the community by the chosen extraction
microbiome of a fish species by direct analysis of the method.
community DNA is shown in Fig. 2. The choice of It is critical to use an appropriate method of extraction
amplicon or shotgun sequencing depends on the goal of the of microbial community DNA which lays the foundation
study. To date, the studies of fish gut microbiome have for accurate characterization of the gut microbiota both
remained limited to deciphering the composition. How- structurally and functionally. Essentially, the sample
ever, shotgun assessments of the gut microbial genetic source and type need to be emphasized upon before relying
repertoire are needed to provide crucial insights into their upon the results from DNA extraction methods comparison
functional potential and can be further aided by the geno- studies as not all the results are comparable owing to the
mic sequencing and analysis of the cultured isolates as has sample variability.
been investigated in other niches [76–85].
The gut produces and receives an arsenal of enzyme
secretions while performing functions such as grinding the Host-Microbe Interactions in Fish Gut
food mechanically and chemically and extracting and
absorbing nutrients, which creates a major challenge in The gut-associated microbes might have potential benefi-
extraction of quality community DNA from the microbial cial or harmful effects on the host. When the beneficial
populations. For instance, bile salts and complex polysac- micro-organisms constitute majority of the microbiome, a
charides present in gut inhibit the downstream processes of state of ‘‘normobiosis’’ prevails. Any perturbations in its
PCR amplification [86]. Therefore, a DNA extraction normal composition result in ‘‘dysbiosis’’ in which state the
method should be employed after envisaging (1) the correct harmful microbes predominate giving rise to a diseased
representation of genomes from entire community with no condition. While on one hand host intrinsic factors and
over or under-representation of individual microbial pop- environment shape the gut microbiome, the microbiota has
ulations, (2) its efficiency on the sample source (foregut, equal influence on the host biology. Thus, a three way
midgut or hindgut) and type (luminal contents only or gut interaction involving host- microbe-environment operates
wall with contents), (3) the design of study which involves to maintain homeostasis in the fish gut.
the type of sequencing i.e., whole genome or targeted Colonization of the gut with specific microorganisms to
sequencing and (4) the quality data required for down- gain insights into the effects of microbiota on host cellular
stream analysis. The choice of DNA extraction method responses in mice revealed that they modulate the expres-
may strongly influence the analysis of the community sion of several cellular genes that endows host with
composition. There are convincing evidences that a method important functions including metabolism, nutrient
for extracting DNA does not conform to changes in host absorption, immune response generation, and intestinal
species or sample type due to variability in the ingested maturation [1]. Similar findings have been obtained using
food and microbial load in the host GI tract [87–90]. As the zebrafish models [23, 91, 92] and in other fish species

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408 Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

Fig. 2 Schematic representation of the workflow for analyzing the into Operational Taxonomic Units (OTUs) and compared against
fish gut microbiome. The currently employed procedures for fish gut databases. The widely used databases and tools include NCBI [126],
microbiome studies include the traditional culture-dependent analysis QIIME [127], UPARSE [128], Silva [129], Green Genes [130], RDP
as well as culture-independent analysis of the total DNA obtained Classifier [131] and Naı̈ve Bayesian Classifier [132]. The community
directly from gut contents and mucosal wall. The culture-dependent is thus profiled based on the relative abundance of each OTU and their
techniques widely use sequencing of 16S rRNA gene to identify phylogenetic relationships. Using advanced ‘omic’ tools, functions of
bacteria. For defining the uncultured microbiota, amplification and the community can also be predicted such as PICRUSt [34] or
sequencing of whole or partial [hypervariable region(s)] of 16S rRNA Tax4Fun [35]. Important microbial functions may then be character-
gene is widely employed. Highly similar sequences are then grouped ized through wet lab experiments

where microorganisms demonstrated to regulate metabo- flora on growth of fish and that the Firmicutes confer fast
lism [29]. Studies on transgenic fast-growing common growth of fish over Bacteroidetes [29]. The microbial
carp, Cyprinus carpio L. suggest an important role of gut members are known to aid in digestion of cellulose in

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Indian J Microbiol (Oct–Dec 2018) 58(4):397–414 409

herbivorous fishes [20, 22, 60]. They are also known to manipulating the gut flora to promote fish health finds
influence innate immune responses in fish [32] and educate important applications in aquaculture. Several Lactobacil-
the host-immune system for better protection against lus species have been identified as probiotics in fish and
pathogenic invaders. These findings provide strong per- other animals including humans [105, 106]. However, their
spectives of the interactions between resident microor- potential needs to be fully explored. Collating inferences
ganisms and their host fish. from different studies would help in identifying microbial
biomarkers and would augment the application of probi-
otics. It is becoming increasingly clear that the microbiome
Conclusion and Future Perspectives: Towards affects its host in more than one ways and its study is
Applied Research thought to bring a plenitude of understanding of its func-
tional potential in the host and expand current notions of the
The gut microbiota is influenced by a myriad of factors but fish gut microbiome.
the appeal of each of these factors on the behavior and
physiology of fish remain poorly understood. For drawing Acknowledgements The authors acknowledge funds from ICAR-
National Bureau of Agriculturally Important Microorganisms
meaningful conclusions, one of the crucial challenges is to NBAIM. CT and SN gratefully acknowledge Council of Scientific &
establish a correlation of microbiome structure and func- Industrial Research (CSIR) and Department of Biotechnology (DBT),
tion with health status, age, genetic background, geo- Govt. of India respectively, for providing doctoral fellowships.
graphical location and other individual differences of the
host. Furthermore, creating a comparative picture based on Author Contributions RL and RKN conceived the idea. CT wrote
the manuscript and SN helped shape the manuscript. RL and RKN
studies employing different methods of DNA extraction critically reviewed the manuscript.
from different sample types within a species needs careful
analyses. As the marker gene based approach limits the Compliance with Ethical Standards
analysis to predictions of microbiome structure, there has
Conflict of interest The authors declare no conflict of interest.
emerged a need for complete shotgun sequencing efforts to
fully explore the metabolic potential of the gut microflora
and uncover functional variation with diet or host associ-
ated factors.
Fish are affected by several pathogenic bacteria includ- References
ing Aeromonas, Edwardsiella, Pseudomonas, Flavobac-
terium, Vibrio and Streptococcus and Yersinia causing 1. Hooper LV, Gordon JI (2001) Commensal host-bacterial rela-
tionships in the gut. Science 292:1115–1118. https://doi.org/10.
diseases in different tropical freshwater fishes [93, 94]. 1126/science.1058709
These are often treated with antibiotics. However, their 2. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, Hoboken
overuse has encouraged antibiotic resistance which makes 3. Suyehiro Y (1942) A study on the digestive system and feeding
the fight against pathogens even more difficult [93]. habits of fish. Jap J Zool 10:1–303
4. Al-Harbi AH, Uddin MN (2004) Seasonal variation in the
Pathogenicity of these bacteria such as Aeromonas hydro- intestinal bacterial flora of hybrid tilapia (Oreochromis niloticus
phila, A. salmonicida, Vibrio anguillarum, V. harveyi, x Oreochromis aureus) cultured in earthern ponds in Saudi
Yersinia ruckeri and Tenacibaculum maritimum is mediated Arabia. Aquaculture 229:37–44. https://doi.org/10.1016/S0044-
by quorum sensing systems that are important for biofilm 8486(03)00388-0
5. Ringo E, Olsen RE, Mayhew TM, Myklebust R (2003) Electron
formation [95]. The use of quorum quenching enzymes has microscopy of the intestinal microflora of fish. Aquaculture
also been successful in reducing pathogenicity of these 227:395–415. https://doi.org/10.1016/j.aquaculture.2003.05.001
pathogens [96–98]. Bacteria derived from fish microbiome 6. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic
have also been shown to produce natural products that identification and in situ detection of individual microbial cells
without cultivation. Microbiol Rev 59:143–169
inhibit formation of biofilms and therefore promote 7. Romero J, Navarrete P (2006) 16S rDNA-based analysis of
detachment of gram-negative pathogens [50]. However, dominant bacterial populations associated with early life stages
more efforts focusing on their application in fish GI tracts of coho salmon (Oncorhynchus kisutch). Microb Ecol
are needed. From the recent studies on isolation of 51:422–430. https://doi.org/10.1007/s00248-006-9037-9
8. Reveco FE, Øverland M, Romarheim OH, Mydland LT (2014)
Bdellovibrios that naturally feed on gram-negative bacteria Intestinal bacterial community structure differs between healthy
from experimental diseased fish models, we envisage the and inflamed intestines in Atlantic salmon (Salmo salar L.).
use of these microbial predators as natural cure of diseases Aquaculture 420–421:262–269. https://doi.org/10.1016/j.aqua
[99–101]. Bdellovibrios are also found to be prevalent in culture.2013.11.007
9. Navarrete P, Espejo RT, Romero J (2009) Molecular analysis of
intestines of human and other animals and have been microbiota along the digestive tract of juvenile Atlantic salmon
reported from diverse habitats [76, 102–104]. The emerging (Salmo salar L.). Microb Ecol 57:550–561. https://doi.org/10.
concept of ‘‘forward microbiomics’’ that involves 1007/s00248-008-9448-x

123
410 Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

10. Stickney RR, Shumway SE (1974) Occurrence of cellulase 26. Ringo E, Sperstad S, Myklebust R, Refstie S, Krogdahl A (2006)
activity in the stomachs of fishes. J Fish Biol 6:779–790. https:// Characterisation of the microbiota associated with intestine of
doi.org/10.1111/j.1095-8649.1974.tb05120.x Atlantic cod (Gadus morhua L.)—the effect of fish meal, stan-
11. Sugita H, Miyajima C, Deguchi Y (1991) The vitamin B12- dard soybean meal and a bioprocessed soybean meal. Aqua-
producing ability of the intestinal microflora of freshwater fish. culture 261:829–841. https://doi.org/10.1016/j.aquaculture.
Aquaculture 92:267–276. https://doi.org/10.1016/0044- 2006.06.030
8486(91)90028-6 27. Givens CE, Ransom B, Bano N, Hollibaugh JT (2014) A fish
12. Nayak SK (2010) Probiotics and immunity: a fish perspective. tale: comparison of the gut microbiomes of 12 finfish and 3
Fish Shellfish Immunol 29:2–14. https://doi.org/10.1016/j.fsi. shark species. Mar Ecol Prog Ser 518:209–223. https://doi.org/
2010.02.017 10.3354/meps11034
13. Ayo-Olalusi CI, Oresegun A, Bernard E (2014) Screening of 28. Desai AR, Links MG, Collins SA, Mansfield GS, Drew MD,
Lactic acid bacteria from the gut of Chrysichthys nigrodigitatus Van Kessel AG, Hill JE (2012) Effects of plant-based diets on
for use as probiotics in aquaculture production. J Fish Aquat Sci the distal gut microbiome of rainbow trout (Oncorhynchus
9:478–482. https://doi.org/10.3923/jfas.2014.478.482 mykiss). Aquaculture 350–353:134–142. https://doi.org/10.1016/
14. Asaduzzaman M, Iehata S, Akter S, Kader MA, Ghosh SK, j.aquaculture.2012.04.005
Khan MNA, Abol-Munafi AB (2018) Effects of host gut-derived 29. Li X, Yan Q, Xie S, Hu W, Yu Y, Hu Z (2013) Gut microbiota
probiotic bacteria on gut morphology, microbiota composition contributes to the growth of fast-growing transgenic common
and volatile short chain fatty acids production of Malaysian carp (Cyprinus carpio L.). PLoS One 8:e64577. https://doi.org/
Mahseer Tor tambroides. Aquac Rep 9:53–61. https://doi.org/ 10.1371/journal.pone.0064577
10.1016/j.aqrep.2017.12.003 30. Carda-Diéguez M, Mira A, Fouz B (2013) Pyrosequencing
15. Star B, Haverkamp THA, Jentoft S, Jakobsen KS (2013) Next survey of intestinal microbiota diversity in cultured sea bass
generation sequencing shows high variation of the intestinal (Dicentrarchus labrax) fed functional diets. FEMS Microbiol
microbial species composition in Atlantic cod caught at a single Ecol 87:451–459. https://doi.org/10.1111/1574-6941.12236
location. BMC Microbiol 13:248. https://doi.org/10.1186/1471- 31. Ingerslev HC, von Gersdorff Jørgensen L, Lenz Strube M,
2180-13-248 Larsen N, Dalsgaard I, Boye M, Madsen L (2014) The devel-
16. Xing MX, Hou ZH, Yuan JB, Liu Y, Qu Y, Liu B (2013) opment of the gut microbiota in rainbow trout (Oncorhynchus
Taxonomic and functional metagenomic profiling of gastroin- mykiss) is affected by first feeding and diet type. Aquaculture
testinal tract microbiome of the farmed adult turbot (Scoph- 424–425:24–34. https://doi.org/10.1016/j.aquaculture.2013.12.
thalmus maximus). FEMS Microbiol Ecol 86:432–443. https:// 032
doi.org/10.1111/1574-6941.12174 32. Gómez GD, Balcázar JL (2008) A review on the interactions
17. Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue between gut microbiota and innate immunity of fish. FEMS
GH (2014) The intestinal microbiome of fish under starvation. Immunol Med Microbiol 52:145–154. https://doi.org/10.1111/j.
BMC Genom 15:266. https://doi.org/10.1186/1471-2164-15-266 1574-695X.2007.00343.x
18. Zarkasi KZ, Abell GC, Taylor RS, Neuman C, Hatje E, Tamplin 33. Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014)
ML, Katouli M, Bowman JP (2014) Pyrosequencing-based Teleost microbiomes: the state of the art in their characteriza-
characterization of gastrointestinal bacteria of Atlantic salmon tion, manipulation and importance in aquaculture and fisheries.
(Salmo salar L.) within a commercial mariculture system. Front Microbiol 5:207. https://doi.org/10.3389/fmicb.2014.
J Appl Microbiol 117:18–27. https://doi.org/10.1111/jam.12514 00207
19. Liu H, Guo X, Gooneratne R, Lai R, Zeng C, Zhan F, Wang W 34. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights
(2016) The gut microbiome and degradation enzyme activity of D, Reyes J, Clemente JC, Burkepile DE, Vega Thurber RL,
wild freshwater fishes influenced by their trophic levels. Sci Rep Knight R, Beiko RG, Huttenhower C (2013) Predictive func-
6:24340. https://doi.org/10.1038/srep24340 tional profiling of microbial communities using 16S rRNA
20. Wu S, Wang G, Angert ER, Wang W, Li W, Zou H (2012) marker gene sequences. Nat Biotechnol 31:814–821. https://doi.
Composition, diversity, and origin of the bacterial community in org/10.1038/nbt.2676
grass carp intestine. PLoS One 7:e30440. https://doi.org/10. 35. Aßhauer KP, Wemheuer B, Daniel R, Meinicke P (2015)
1371/journal.pone.0030440 Tax4Fun: predicting functional profiles from metagenomic 16S
21. Tarnecki AM, Burgos FA, Ray CL, Arias CR (2017) Fish rRNA data. Bioinformatics 31:2882–2884. https://doi.org/10.
intestinal microbiome: diversity and symbiosis unravelled by 1093/bioinformatics/btv287
metagenomics. J Appl Microbiol 123:2–17. https://doi.org/10. 36. Li H, Zheng Z, Cong-xin X, Bo H, Chao-yuan W, Gang H
1111/jam.13415 (2009) Isolation of cellulose-producing microbes from the
22. Nayak SK (2010) Role of gastrointestinal microbiota in fish. intestine of grass carp (Ctenopharyngodon idellus). Environ Biol
Aquac Res 41:1553–1573. https://doi.org/10.1111/j.1365-2109. Fishes 86:131–135. https://doi.org/10.1007/978-90-481-3458-8_
2010.02546.x 19
23. Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish 37. Li H, Wu S, Wirth S, Hao Y, Wang W, Zou H, Li W, Wang G
reveal evolutionarily conserved responses to the gut microbiota. (2016) Diversity and activity of cellulolytic bacteria, isolated
Proc Natl Acad Sci USA 101:4596–4601. https://doi.org/10. from the gut contents of grass carp (Ctenopharyngodon idellus)
1073/pnas.0400706101 (Valenciennes) fed on Sudan grass (Sorghum sudanense) or
24. Sullam KE, Essinger SD, Lozupone CA, O’Connor MP, Rosen artificial feedstuffs. Aquac Res 47:153–164. https://doi.org/10.
GL, Knight R, Kilham SS, Russell JA (2012) Environmental and 1111/are.12478
ecological factors that shape the gut bacterial communities of 38. McDonald R, Schreier HJ, Watts JE (2012) Phylogenetic anal-
fish: a meta-analysis. Mol Ecol 21:3363–3378. https://doi.org/ ysis of microbial communities in different regions of the gas-
10.1111/j.1365-294X.2012.05552.x trointestinal tract in Panaque nigrolineatus, a wood-eating fish.
25. Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh PLoS One 7:e48018. https://doi.org/10.1371/journal.pone.
CM, Guillemin K, Rawls JF (2011) Evidence for a core gut 0048018
microbiota in the zebrafish. ISME J 5:1595–1608. https://doi. 39. Watts JEM, McDonald R, Daniel R, Schreier HJ (2013)
org/10.1038/ismej.2011.38 Examination of a culturable microbial population from the

123
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414 411

gastrointestinal tract of the wood-eating loricariid cat- behavior of invasive Asian carp and indigenous American fish.
fish Panaque nigrolineatus. Diversity 5:641–656. https://doi. ISME J 8:541–551. https://doi.org/10.1038/ismej.2013.181
org/10.3390/d5030641 54. Wong S, Rawls JF (2012) Intestinal microbiota composition in
40. Clements KD, Pasch IBY, Moran D, Turner SJ (2007) Clostridia fishes is influenced by host ecology and environment. Mol Ecol
dominate 16S rRNA gene libraries prepared from the hindgut of 21:3100–3102. https://doi.org/10.1111/j.1365-294X.2012.
temperate marine herbivorous fishes. Mar Biol 150:1431–1440. 05646.x
https://doi.org/10.1007/s00227-006-0443-9 55. Rawls JF, Mahowald MA, Ley RE, Gordon JI (2006) Reciprocal
41. Catalan N, Villasante A, Wacyk J, Ramı́rez C, Romero J (2017) gut microbiota transplants from zebrafish and mice to germ-free
Fermented soybean meal increases lactic acid bacteria in gut recipients reveal host habitat selection. Cell 127:423–433.
microbiota of Atlantic Salmon (Salmo salar). Probiot Antimi- https://doi.org/10.1016/j.cell.2006.08.043
crob Proteins. https://doi.org/10.1007/s12602-017-9366-7 56. Hennersdorf P, Kleinertz S, Theisen S, Abdul-Aziz MA, Mrot-
42. Montalban-Arques A, De Schryver P, Bossier P, Gorkiewicz G, zek G, Palm HW, Saluz HP (2016) Microbial diversity and
Mulero V, Gatlin DM, Galindo-Villegas J (2015) Selective parasitic load in tropical fish of different environmental condi-
manipulation of the gut microbiota improves immune status in tions. PLoS One 11:e0151594. https://doi.org/10.1371/journal.
vertebrates. Front Immunol 6:512. https://doi.org/10.3389/ pone.0151594
fimmu.2015.00512 57. Miyake S, Ngugi DK, Stingl U (2015) Diet strongly influences
43. Maji A, Misra R, Dhakan DB, Gupta V, Mahato NK, Saxena R, the gut microbiota of surgeonfishes. Mol Ecol 24:656–672.
Mittal P, Thukral N, Sharma E, Singh A, Virmani R, Gaur M, https://doi.org/10.1111/mec.13050
Singh H, Hasija Y, Arora G, Agrawal A, Chaudhry A, Khurana 58. Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH (2013)
JP, Sharma VK, Lal R, Singh Y (2018) Gut microbiome con- The influence of diet on the gut microbiota. Pharmacol Res
tributes to impairment of immunity in pulmonary tuberculosis 69:52–60. https://doi.org/10.1016/j.phrs.2012.10.020
patients by alteration of butyrate and propionate producers. 59. Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R,
Environ Microbiol 20:402–419. https://doi.org/10.1111/1462- Caporaso JG, Svanback R (2014) Individuals’ diet diversity
2920.14015 influences gut microbial diversity in two freshwater fish
44. Yan Q, Li J, Yu Y, Wang J, He Z, Van Nostrand JD, Kempher (threespine stickleback and Eurasian perch). Ecol Lett
ML, Wu L, Wang Y, Liao L, Li X, Wu S, Ni J, Wang C, Zhou J 17:979–987. https://doi.org/10.1111/ele.12301
(2016) Environmental filtering decreases with fish development 60. Saha S, Roy RN, Sen SK, Ray AK (2006) Characterization of
for the assembly of gut microbiota. Environ Microbiol cellulase-producing bacteria from the digestive tract of
18:4739–4754. https://doi.org/10.1111/1462-2920.13365 tilapia, Oreochromis mossambica (Peters) and grass
45. Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, carp, Ctenopharyngodon idella (Valenciennes). Aquac Res
Guillemin K, Bohannan BJ (2016) Contribution of neutral pro- 37:380–388. https://doi.org/10.1111/j.1365-2109.2006.01442.x
cesses to the assembly of gut microbial communities in the 61. Dehler CE, Secombes CJ, Martin SA (2017) Environmental and
zebrafish over host development. ISME J 10:655–664. https:// physiological factors shape the gut microbiota of Atlantic sal-
doi.org/10.1038/ismej.2015.142 mon parr (Salmo salar L.). Aquaculture 467:149–157. https://
46. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evo- doi.org/10.1016/j.aquaculture.2016.07.017
lutionary forces shaping microbial diversity in the human 62. Li X, Zhou L, Yu Y, Ni J, Xu W, Yan Q (2017) Composition of
intestine. Cell 124:837–848. https://doi.org/10.1016/j.cell.2006. Gut microbiota in the gibel carp (Carassius auratus gibelio)
02.017 varies with host development. Microb Ecol 74:239–249. https://
47. Rieu A, Aoudia N, Jego G, Chluba J, Yousfi N, Briandet R, doi.org/10.1007/s00248-016-0924-4
Deschamps J, Gasquet B, Monedero V, Garrido C, Guzzo J 63. Giatsis C, Sipkema D, Smidt H, Heilig H, Benvenuti G, Verreth
(2014) The biofilm mode of life boosts the anti-inflammatory J, Verdegem M (2015) The impact of rearing environment on
properties of Lactobacillus. Cell Microbiol 16:1836–1853. the development of gut microbiota in tilapia larvae. Sci Rep
https://doi.org/10.1111/cmi.12331 5:18206. https://doi.org/10.1038/srep18206
48. de Vos WM (2015) Microbial biofilms and the human intestinal 64. Eichmiller JJ, Hamilton MJ, Staley C, Sadowsky MJ, Sorensen
microbiome. NPJ Biofilms Microbiomes 1:15005. https://doi. PW (2016) Environment shapes the fecal microbiome of inva-
org/10.1038/npjbiofilms.2015.5 sive carp species. Microbiome 4:44. https://doi.org/10.1186/
49. Kalia VC, Prakash J, Koul S, Ray S (2017) Simple and rapid s40168-016-0190-1
method for detecting biofilm forming bacteria. Indian J Micro- 65. Schmidt VT, Smith KF, Melvin DW, Amaral-Zettler LA (2015)
biol 57:109–111. https://doi.org/10.1007/s12088-016-0616-2 Community assembly of a euryhaline fish microbiome during
50. Sanchez LM, Cheng AT, Warner CJ, Townsley L, Peach KC, salinity acclimation. Mol Ecol 24:2537–2550. https://doi.org/10.
Navarro G, Shikuma NJ, Bray WM, Riener RM, Yildiz FH, 1111/mec.13177
Linington RG (2016) Biofilm formation and detachment in 66. Sylvain FÉ, Cheaib B, Llewellyn M, Correia TG, Fagundes DB,
gram-negative pathogens is modulated by select bile acids. Val AL, Derome N (2016) pH drop impacts differentially skin
PLoS One 11:e0149603. https://doi.org/10.1371/journal.pone. and gut microbiota of the Amazonian fish tambaqui (Colossoma
0149603 macropomum). Sci Rep 6:32032. https://doi.org/10.1038/
51. Larsen AM, Mohammed HH, Arias CR (2014) Comparison of srep32032
DNA extraction protocols for the analysis of gut microbiota in 67. Li X, Yu Y, Feng W, Yan Q, Gong Y (2012) Host species as a
fishes. FEMS Microbiol Lett 362:fnu031. https://doi.org/10. strong determinant of the intestinal microbiota of fish larvae.
1093/femsle/fnu031 J Microbiol 50:29–37. https://doi.org/10.1007/s12275-012-
52. Gajardo K, Rodiles A, Kortner TM, Krogdahl Å, Bakke AM, 1340-1
Merrifield DL, Sørum H (2016) A high-resolution map of the 68. Li XM, Zhu YJ, Yan QY, Ringø E, Yang DG (2014) Do the
gut microbiota in Atlantic salmon (Salmo salar): a basis for intestinal microbiotas differ between paddlefish (Polyodon
comparative gut microbial research. Sci Rep 6:30893. https:// spathala) and bighead carp (Aristichthys nobilis) reared in the
doi.org/10.1038/srep30893 same pond? J Appl Microbiol 117:1245–1252. https://doi.org/
53. Ye L, Amberg J, Chapman D, Gaikowski M, Liu WT (2014) 10.1111/jam.12626
Fish gut microbiota analysis differentiates physiology and

123
412 Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

69. Wong S, Waldrop T, Summerfelt S, Davidson J, Barrows F, Hexachlorocyclohexane (HCH) contaminated pond soil. J Mi-
Kenney PB, Welch T, Wiens GD, Snekvik K, Rawls JF, Good C crobiol 51:689–694. https://doi.org/10.1007/s12275-013-2705-9
(2013) Aquacultured rainbow trout (Oncorhynchus mykiss) 83. Dua A, Sangwan N, Kaur J, Saxena A, Kohli P, Gupta AK, Lal
possess a large core intestinal microbiota that is resistant to R (2013) Draft genome sequence of Agrobacterium sp. Strain
variation in diet and rearing density. Appl Environ Microbiol UHFBA-218, isolated from rhizosphere soil of crown gall-in-
79:4974–4984. https://doi.org/10.1128/AEM.00924-13 fected cherry rootstock colt. Genome Announc 1:e00302–
70. Sullam KE, Rubin BE, Dalton CM, Kilham SS, Flecker AS, e00313. https://doi.org/10.1128/genomeA.00302-13
Russell JA (2015) Divergence across diet, time and populations 84. Negi V, Lata P, Sangwan N, Gupta S, Das S, Rao DLN, Lal R
rules out parallel evolution in the gut microbiomes of Trinida- (2014) Draft genome sequence of Hexachlorocyclohexane
dian guppies. ISME J 9:1508–1522. https://doi.org/10.1038/ (HCH)-degrading Sphingobium lucknowense strain F2, isolated
ismej.2014.231 from the HCH dumpsite. Genome Announc 2:e00788-14.
71. Li T, Long M, Li H, Gatesoupe FJ, Zhang X, Zhang Q, Feng D, https://doi.org/10.1128/genomeA.00788-14
Li A (2017) Multi-omics analysis reveals a correlation between 85. Sharma A, Hira P, Shakarad M, Lal R (2014) Draft genome
the host phylogeny, gut microbiota and metabolite profiles in sequence of Cellulosimicrobium sp. MM, isolated from arsenic
cyprinid fishes. Front Microbiol 8:454. https://doi.org/10.3389/ rich microbial mats of a Himalayan hot spring. Genome
fmicb.2017.00454 Announc 5:e01020-14. https://doi.org/10.1128/genomeA.01020-
72. Michl SC, Ratten JM, Beyer M, Hasler M, LaRoche J, Schulz C 14
(2017) The malleable gut microbiome of juvenile rainbow trout 86. Schrader C, Schielke A, Ellerbroek L, Johne R (2012) PCR
(Oncorhynchus mykiss): diet-dependent shifts of bacterial inhibitors—occurrence, properties and removal. J Appl Micro-
community structures. PLoS One 12:e0177735. https://doi.org/ biol 113:1014–1026. https://doi.org/10.1111/j.1365-2672.2012.
10.1371/journal.pone.0177735 05384.x
73. Mansfield GS, Desai AR, Nilson SA, Van Kessel AG, Drew 87. Kashinskaya EN, Andree KB, Simonov EP, Solovyev MM
MD, Hill JE (2010) Characterization of rainbow trout (On- (2017) DNA extraction protocols may influence biodiversity
corhynchus mykiss) intestinal microbiota and inflammatory detected in the intestinal microbiome: a case study from wild
marker gene expression in a recirculating aquaculture system. Prussian carp. Carassius gibelio. FEMS Microbiol Ecol
Aquaculture 307:95–104. https://doi.org/10.1016/j.aquaculture. 93:fiw240. https://doi.org/10.1093/femsec/fiw240
2010.07.014 88. Hart ML, Meyer A, Johnson PJ, Ericsson AC (2015) Compar-
74. Ringø E, Zhou Z, Vecino JLG, Wadsworth S, Romero J, ative evaluation of DNA extraction methods from feces of
Krogdahl Å, Olsen RE, Dimitroglou A, Foey A, Davies S, Owen multiple host species for downstream next-generation sequenc-
M, Lauzon HL, Martinsen LL, De Schryver P, Bossier P, ing. PLoS One 10:e0143334. https://doi.org/10.1371/journal.
Sperstad S, Merrifield DL (2016) Effect of dietary components pone.0143334
on the gut microbiota of aquatic animals. A never-ending story? 89. Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel
Aquac Nutr 22:219–282. https://doi.org/10.1111/anu.12346 SJ, Waghorn GC, Janssen PH (2013) Effect of DNA extraction
75. Rajendhran J, Gunasekaran P (2010) Human microbiomics. methods and sampling techniques on the apparent structure of
Indian J Microbiol 50:109–112. https://doi.org/10.1007/s12088- cow and sheep rumen microbial communities. PLoS One
010-0034-9 8:e74787. https://doi.org/10.1371/journal.pone.0074787
76. Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, 90. Mirsepasi H, Persson S, Struve C, Andersen LOB, Petersen AM,
Khurana JP, Sockett RE, Gilbert JA, Lal R (2015) Arsenic rich Krogfelt KA (2014) Microbial diversity in fecal samples
Himalayan hot spring metagenomics reveal genetically novel depends on DNA extraction method: easyMag DNA extraction
predator-prey genotypes. Environ Microbiol Rep 7:812–823. compared to QIAamp DNA stool mini kit extraction. BMC Res
https://doi.org/10.1111/1758-2229.12297 Notes 7:50. https://doi.org/10.1186/1756-0500-7-50
77. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J 91. Kanther M, Rawls JF (2010) Host-microbe interactions in the
(2012) Comparative metagenomic analysis of soil microbial developing zebrafish. Curr Opin Immunol 22:10–19. https://doi.
communities across three hexachlorocyclohexane contamination org/10.1016/j.coi.2010.01.006
levels. PLoS One 7:e46219. https://doi.org/10.1371/journal. 92. Cheesman SE, Guillemin K (2007) We know you are in there:
pone.0046219 conversing with the indigenous gut microbiota. Res Microbiol
78. Dwivedi V, Sangwan N, Nigam A, Garg N, Niharika N, Khu- 158:2–9. https://doi.org/10.1016/j.resmic.2006.10.005
rana P, Khurana JP, Lal R (2012) Draft genome sequence of 93. Kalia VC (2014) Microbes, antimicrobials and resistance: the
Thermus sp. RL isolated from hot water spring located atop the battle goes on. Indian J Microbiol 54:1–2. https://doi.org/10.
Himalayan ranges at Manikaran, India. J Bacteriol 1007/s12088-013-0443-7
194:3534–3535. https://doi.org/10.1128/JB.00604-12 94. Austin B (2011) Taxonomy of bacterial fish pathogens. Vet Res
79. Singh AK, Sangwan N, Sharma A, Gupta V, Khurana JP, Lal R 42:20. https://doi.org/10.1186/1297-9716-42-20
(2013) Draft genome sequence of Sphingobium quisquiliarum 95. Kalia VC (2013) Quorum sensing inhibitors: an overview.
P25T, a novel Hexachlorocylohexane (HCH) degrading bac- Biotechnol Adv 31:224–245. https://doi.org/10.1016/j.bio
terium isolated from the HCH dumpsite. Genome Announc techadv.2012.10.004
1:e00717-12. https://doi.org/10.1128/genomeA.00717-13 96. Koul S, Kalia VC (2017) Multiplicity of quorum quenching
80. Mukherjee U, Kumar R, Mahato NK, Khurana JP, Lal R (2013) enzymes: a potential mechanism to limit quorum sensing bac-
Draft genome sequence of Sphingobium sp. HDIPO4, an avid terial population. Indian J Microbiol 57:100–108. https://doi.
degrader of Hexachlorocyclohexane. Genome Announc org/10.1007/s12088-016-0633-1
1:e00749-13. https://doi.org/10.1128/genomeA.00749-13 97. Kalia VC, Purohit HJ (2011) Quenching the quorum sensing
81. Kaur J, Verma H, Tripathi C, Khurana JP, Lal R (2013) Draft system: potential antibacterial drug targets. Crit Rev Microbiol
genome sequence of a Hexachlorocyclohexane-degrading bac- 37:121–140. https://doi.org/10.3109/1040841X.2010.532479
terium, Sphingobium baderi strain LL03T. Genome Announc 98. Chu W, Lu F, Zhu W, Kang C (2011) Isolation and character-
1:e00751-13. https://doi.org/10.1128/genomeA.00751-13 ization of new potential probiotic bacteria based on quorum-
82. Dua A, Malhotra J, Saxena A, Khan F, Lal R (2013) Devosia sensing system. J Appl Microbiol 110:202–208. https://doi.org/
lucknowensis sp. nov., a bacterium isolated from 10.1111/j.1365-2672.2010.04872.x

123
Indian J Microbiol (Oct–Dec 2018) 58(4):397–414 413

99. Willis AR, Moore C, Mazon-Moya M, Krokowski S, Lambert C, microbiota in zebrafish. ISME J 11:1630–1639. https://doi.org/
Till R, Mostowy S, Sockett RE (2016) Injections of predatory 10.1038/ismej.2017.28
bacteria work alongside host immune cells to treat Shigella 114. Gajardo K, Jaramillo-Torres A, Kortner TM, Merrifield DL,
infection in Zebrafish larvae. Curr Biol 26:3343–3351. https:// Tinsley J, Bakke AM, Krogdahl Å (2017) Alternative protein
doi.org/10.1016/j.cub.2016.09.067 sources in the diet modulate microbiota and functionality in the
100. Cao H, He S, Wang H, Hou S, Lu L, Yang X (2012) distal intestine of Atlantic salmon (Salmo salar). Appl Environ
Bdellovibrios, potential biocontrol bacteria against pathogenic Microbiol 83:e02615–e02616. https://doi.org/10.1128/AEM.
Aeromonas hydrophila. Vet Microbiol 154:413–418. https://doi. 02615-16
org/10.1016/j.vetmic.2011.07.032 115. Zhai Q, Yu L, Li T, Zhu J, Zhang C, Zhao J, Zhang H, Chen W
101. Chu WH, Zhu W (2010) Isolation of Bdellovibrio as biological (2017) Effect of dietary probiotic supplementation on intestinal
therapeutic agents used for the treatment of Aeromonas hydro- microbiota and physiological conditions of Nile tilapia (Ore-
phila infection in fish. Zoonoses Public Health 57:258–264. ochromis niloticus) under waterborne cadmium exposure.
https://doi.org/10.1111/j.1863-2378.2008.01224.x Antonie Van Leeuwenhoek 110:501–513. https://doi.org/10.
102. Feng S, Tan CH, Cohen Y, Rice SA (2016) Isolation of 1007/s10482-016-0819-x
Bdellovibrio bacteriovorus from a tropical wastewater treatment 116. Lyons PP, Turnbull JF, Dawson KA, Crumlish M (2017) Phy-
plant and predation of mixed species biofilms assembled by the logenetic and functional characterization of the distal intestinal
native community members. Environ Microbiol 18:3923–3931. microbiome of rainbow trout Oncorhynchus mykiss from both
https://doi.org/10.1111/1462-2920.13384 farm and aquarium settings. J Appl Microbiol 122:347–363.
103. Oyedara OO, De Luna-Santillana EJ, Olguin-Rodriguez O, Guo https://doi.org/10.1111/jam.13347
X, Mendoza-Villa MA et al (2016) Isolation of Bdellovibrio sp. 117. Song W, Li L, Huang H, Jiang K, Zhang F, Chen X, Zhao M,
from soil samples in Mexico and their potential applications in Ma L (2016) The gut microbial community of Antarctic fish
control of pathogens. Microbiologyopen 5:992–1002. https:// detected by 16S rRNA gene sequence analysis. Biomed Res Int
doi.org/10.1002/mbo3.382 2016:3241529. https://doi.org/10.1155/2016/3241529
104. Iebba V, Santangelo F, Totino V, Nicoletti M, Gagliardi A et al 118. Bledsoe JW, Peterson BC, Swanson KS, Small BC (2016)
(2013) Higher prevalence and abundance of Bdellovibrio bac- Ontogenetic characterization of the intestinal microbiota of
teriovorus in the human gut of healthy subjects. PLoS One channel catfish through 16S rRNA gene sequencing reveals
8:e61608. https://doi.org/10.1371/journal.pone.0061608 insights on temporal shifts and the influence of environmental
105. He S, Ran C, Qin C, Li S, Zhang H, de Vos WM, Ringø E, Zhou microbes. PLoS One 11:e0166379. https://doi.org/10.1371/jour
Z (2017) Anti-infective effect of adhesive probiotic Lacto- nal.pone.0166379
bacillus in fish is correlated with their spatial distribution in the 119. Giatsis C, Sipkema D, Ramiro-Garcia J, Bacanu GM, Abernathy
intestinal tissue. Sci Rep 7:13195. https://doi.org/10.1038/ J, Verreth J, Smidt H, Verdegem M (2016) Probiotic legacy
s41598-017-13466-1 effects on gut microbial assembly in tilapia larvae. Sci Rep
106. Koul S, Kalia VC (2016) Comparative genomics reveals 6:33965. https://doi.org/10.1038/srep33965
biomarkers to identify Lactobacillus species. Indian J Microbiol 120. Gatesoupe FJ, Huelvan C, Le Bayon N, Le Delliou H, Madec L,
56:265–276. https://doi.org/10.1007/s12088-016-0605-5 Mouchel O, Quazuguel P, Mazurais D, Zambonino-Infante JL
107. Zhang Z, Li D, Refaey MM, Xu W, Tang R, Li L (2018) Host (2016) The highly variable microbiota associated to intestinal
age affects the development of southern catfish gut bacterial mucosa correlates with growth and hypoxia resistance of sea
community divergent from that in the food and rearing water. bass, Dicentrarchus labrax, submitted to different nutritional
Front Microbiol 9:495. https://doi.org/10.3389/fmicb.2018. histories. BMC Microbiol 16:266. https://doi.org/10.1186/
00495 s12866-016-0885-2
108. Zhang Z, Li D, Refaey MM, Xu W (2017) High spatial and 121. Stephens WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guil-
temporal variations of microbial community along the southern lemin K, Bohannan BJM (2016) The composition of the zebrafish
catfish gastrointestinal tract: insights into dynamic food diges- intestinal microbial community varies across development. ISME J
tion. Front Microbiol 8:1531. https://doi.org/10.3389/fmicb. 10:644–654. https://doi.org/10.1038/ismej.2015.140
2017.01531 122. Schmidt V, Amaral-Zettler L, Davidson J, Summerfelt S, Good
109. Koo H, Hakim JA, Powell ML, Kumar R, Eipers PG, Morrow C (2016) Influence of fishmeal-free diets on microbial com-
CD, Crowley M, Lefkowitz EJ, Watts SA, Bej AK (2017) munities in Atlantic Salmon (Salmo salar) recirculation aqua-
Metagenomics approach to the study of the gut microbiome culture systems. Appl Environ Microbiol 82:4470–4481. https://
structure and function in zebrafish Danio rerio fed with gluten doi.org/10.1128/AEM.00902-16
formulated diet. J Microbiol Methods 135:69–76. https://doi.org/ 123. Zarkasi KZ, Taylor RS, Abell GC, Tamplin ML, Glencross BD,
10.1016/j.mimet.2017.01.016 Bowman JP (2016) Atlantic Salmon (Salmo salar L.) gastroin-
110. Nielsen S, Walburn JW, Vergés A, Thomas T, Egan S (2017) testinal microbial community dynamics in relation to digesta
Microbiome patterns across the gastrointestinal tract of the properties and diet. Microb Ecol 71:589–603. https://doi.org/10.
rabbitfish Siganus fuscescens. PeerJ 5:e3317. https://doi.org/10. 1007/s00248-015-0728-y
7717/peerj.3317 124. Llewellyn MS, McGinnity P, Dionne M, Letourneau J, Thonier
111. Carlson JM, Leonard AB, Hyde ER, Petrosino JF, Primm TP F, Carvalho GR, Creer S, Derome N (2016) The biogeography
(2017) Microbiome disruption and recovery in the fish Gam- of the atlantic salmon (Salmo salar) gut microbiome. ISME J
busia affinis following exposure to broad-spectrum antibiotic. 10:1280–1284. https://doi.org/10.1038/ismej.2015.189
Infect Drug Resist 10:143–154. https://doi.org/10.2147/IDR. 125. Narrowe AB, Albuthi-Lantz M, Smith EP, Bower KJ, Roane
S129055 TM, Vajda AM, Miller CS (2015) Perturbation and restoration
112. Li T, Li H, Gatesoupe FJ, She R, Lin Q, Yan X, Li J, Li X of the fathead minnow gut microbiome after low-level triclosan
(2017) Bacterial signatures of ‘‘Red-Operculum’’ disease in the exposure. Microbiome 3:6. https://doi.org/10.1186/s40168-015-
gut of crucian carp (Carassius auratus). Microb Ecol 0069-6
74:510–521. https://doi.org/10.1007/s00248-017-0967-1 126. NCBI Resource Coordinators (2016) Database resources of the
113. Stagaman K, Burns AR, Guillemin K, Bohannan BJ (2017) The National Center for Biotechnology Information. Nucleic Acids
role of adaptive immunity as an ecological filter on the gut Res 44:D7–D19. https://doi.org/10.1093/nar/gkv1290

123
414 Indian J Microbiol (Oct–Dec 2018) 58(4):397–414

127. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman Greengenes, a chimera-checked 16S rRNA gene database and
FD et al (2010) QIIME allows analysis of high-throughput workbench compatible with ARB. Appl Environ Microbiol
community sequencing data. Nat Methods 7:335–336. https:// 72:5069–5072. https://doi.org/10.1128/AEM.03006-05
doi.org/10.1038/nmeth.f.303 131. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-
128. Edgar RC (2013) UPARSE: highly accurate OTU sequences Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM,
from microbial amplicon reads. Nat Methods 10:996–998. Tiedje JM (2009) The Ribosomal Database Project: improved
https://doi.org/10.1038/nmeth.2604 alignments and new tools for rRNA analysis. Nucleic Acids Res
129. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, 37:D141–D145. https://doi.org/10.1093/nar/gkn879
Glöckner FO (2007) SILVA: a comprehensive online resource 132. Rosen GL, Reichenberger ER, Rosenfeld AM (2011) NBC: the
for quality checked and aligned ribosomal RNA sequence data Naive Bayes classification tool webserver for taxonomic clas-
compatible with ARB. Nucleic Acids Res 35:7188–7196. sification of metagenomic reads. Bioinformatics 27:127–129.
https://doi.org/10.1093/nar/gkm864 https://doi.org/10.1093/bioinformatics/btq619
130. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL,
Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006)

123