Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

Lurie-Weinberger, Mor N; Peeri, Michael; Gophna, Uri

doi:10.1016/j.ygeno.2011.10.005

Cited by 32 publications

(33 citation statements)

References 20 publications

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“…It was speculated that these genes give their host an advantage in the gut niche, enabling it to vary surface structures, especially capsular polysaccharides, in vivo. Other enriched subsystems included "Amino Acids" and "Protein Metabolism," which were predominantly constituted of biosynthetic pathway functions, which may grant their hosts an advantage in the rumen, as recently suggested (51). On the other hand, the "Carbohydrates" subsystem was composed mainly of sugars using Fig.…”

Section: Discussionmentioning

confidence: 74%

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Insights into the bovine rumen plasmidome

Kav

Sasson

Jami

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

137

115

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Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.

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Section: Discussionmentioning

confidence: 74%

“…3). This enzyme and other members of this subsystem have been recently reported to be laterally transferred in the human gut from bacteria into archaeal genomes (51). It was speculated that these genes give their host an advantage in the gut niche, enabling it to vary surface structures, especially capsular polysaccharides, in vivo.…”

Section: Discussionmentioning

confidence: 99%

Insights into the bovine rumen plasmidome

Kav

Sasson

Jami

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

137

115

View full text Add to dashboard Cite

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“…Mobile genetic elements have been associated with LGT of glycosyltransferases, adhesion-like proteins and ABC transporters among different bacterial species (Lurie-Weinberger et al, 2012). Transposases or other insertion elements normally flank genes subjected to LGT (Schwendener & Perreten, 2011).…”

Section: Discussionmentioning

confidence: 99%

Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen

et al. 2014

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Haemophilus parasuis is the causative agent of Glä sser's disease, a systemic disorder characterized by polyarthritis, polyserositis and meningitis in pigs. Although it is well known that H. parasuis serovar 5 is the most prevalent serovar associated with the disease, the genetic differences among strains are only now being discovered. Genomes from two serovar 5 strains, SH0165 and 29755, are already available. Here, we present the draft genome of a third H. parasuis serovar 5 strain, the formal serovar 5 reference strain Nagasaki. An in silico genome subtractive analysis with full-length predicted genes of the three H. parasuis serovar 5 strains detected 95, 127 and 95 strain-specific genes (SSGs) for Nagasaki, SH0165 and 29755, respectively. We found that the genomic diversity within these three strains was high, in part because of a high number of mobile elements. Furthermore, a detailed analysis of large sequence polymorphisms (LSPs), encompassing regions ranging from 2 to 16 kb, revealed LSPs in virulence-related elements, such as a Toll-IL receptor, the AcrA multidrug efflux protein, an ATPbinding cassette (ABC) transporter, lipopolysaccharide-synthetizing enzymes and a tripartite ATP-independent periplasmic (TRAP) transporter. The whole-genome codon adaptation index (CAI) was also calculated and revealed values similar to other well-known bacterial pathogens. In addition, whole-genome SNP analysis indicated that nucleotide changes tended to be increased in membrane-related genes. This analysis provides further evidence that the genome of H. parasuis has been subjected to multiple lateral gene transfers (LGTs) and to fine-tuning of virulence factors, and has the potential for accelerated genome evolution.

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“…The nitrate/sulfonate/bicarbonate ABC transporter, which also can be found in strain ST-III, is up-regulated in response to salt-stress (Huang et al, 2006). It may increase the efficiency of inorganic salt uptake and give the bacteria a way to survive and compete in the gut niche (Lurie-Weinberger et al, 2012). Two genes, zj316_2874 and zj316_2875, code the ImpB/MucB/SamB family proteins, which are involved in ultraviolet (UV) protection.…”

Section: Stress Responsementioning

confidence: 99%

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles

et al. 2016

J. Zhejiang Univ. Sci. B

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Abstract:Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

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Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

Cited by 32 publications

References 20 publications

Insights into the bovine rumen plasmidome

Insights into the bovine rumen plasmidome

Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles

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