Papers by Dr Shahid Manzoor
Associated MIGS record. (DOCX 124Â kb)
Standards in genomic sciences, 2015
Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belo... more Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are presenting assembly and annotation features as well as basic genomic properties of the type strain Sp3.
Genome Announcements, 2013
We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant growt... more We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant growth-promoting bacterium isolated from a cotton plant. Its genome contains gene clusters involved in nonribosomal synthesis of secondary metabolites known for their antimicrobial activities. The availability of this genome will provide novel insights into plant-bacterium–associated activities.
EMBnet.journal, 2013
Table 1. Genomic features of SAOB Genome. Strain T. size (bp) T. Protein coding genes Avg. CDS Lg... more Table 1. Genomic features of SAOB Genome. Strain T. size (bp) T. Protein coding genes Avg. CDS Lgth. Avg. Interg. Lgth. Total rRNAs Total tRNAs Protein Coding Density G+C %
Computational and Comparative Investigations of Syntrophic Acetate-oxidising Bacteria (SAOB)-Geno... more Computational and Comparative Investigations of Syntrophic Acetate-oxidising Bacteria (SAOB)-Genome-guided analysis of metabolic capacities and energy conserving systems.
Genome announcements, Jan 6, 2014
Clostridium ultunense BS is the first isolated strain (type strain) of C. ultunense that was iden... more Clostridium ultunense BS is the first isolated strain (type strain) of C. ultunense that was identified as a mesophilic syntrophic acetate-oxidizing bacterium (SAOB). Here, we report the draft genome sequence of this strain, which will help us to elucidate the mechanism of syntrophic acetate oxidization.
Journal of Biotechnology, 2009
The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium... more The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plantbacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.
PLOS ONE, 2016
Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO... more Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO 2 and H 2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F 1 F 0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The
Standards in Genomic Sciences, 2015
Treponema phagedenis' is considered to be a key agent in the pathogenesis of bovine digital derma... more Treponema phagedenis' is considered to be a key agent in the pathogenesis of bovine digital dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby report the draft sequence of 'T. phagedenis' strain V1. The draft genome assembly consists of 51 scaffolds comprising 3,129,551 bp and a GC-content of 39.9 %. Putative pathogenicity related factors have been identified in the genome that can be used in future studies to gain insight into the pathogenic mechanisms of 'T. phagedenis'.
PloS one, 2015
This paper describes the genome-based analysis of Tepidanaerobacter acetatoxydans strain Re1, a s... more This paper describes the genome-based analysis of Tepidanaerobacter acetatoxydans strain Re1, a syntrophic acetate-oxidising bacterium (SAOB). Principal issues such as environmental adaptations, metabolic capacities, and energy conserving systems have been investigated and the potential consequences for syntrophic acetate oxidation discussed. Briefly, in pure culture, T. acetatoxydans grows with different organic compounds and produces acetate as the main product. In a syntrophic consortium with a hydrogenotrophic methanogen, it can also reverse its metabolism and instead convert acetate to formate/H2 and CO2. It can only proceed if the product formed is continuously removed. This process generates a very small amount of energy that is scarcely enough for growth, which makes this particular syntrophy of special interest. As a crucial member of the biogas-producing community in ammonium-rich engineered AD processes, genomic features conferring ammonium resistance, bacterial defense, ...
Genome announcements, 2013
Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for efficient ... more Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for efficient biogas production from protein-rich materials. Tepidanaerobacter acetatoxydans is the first reported SAOB for which the genome has been sequenced. Genome analysis will aid us in understanding the mechanisms regulating syntrophy, particularly energy-conserving and electron transfer mechanisms.
Standards in Genomic Sciences, 2014
Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to pr... more Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to promote host plant g rowth throug h production of stimulating compounds and suppression of soil borne pathogens by synthesizing antibacterial and antifung al metabolites or priming plant defense as induced systemic resistance. The g enome of B. amyloliquefaciens UCMB5033 comprises a 4,071,167 bp long circular chromosome that consists of 3,912 protein-coding genes, 86 tRNA g enes and 10 rRNA operons.
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Papers by Dr Shahid Manzoor