Structure of the human gastric bacterial community in relation to <i>Helicobacter pylori</i> status

Maldonado‐Contreras, Ana; Goldfarb, Kate C.; Godoy-Vitorino, Filipa; Karaöz, Ulaş; Contreras, Mónica; Blaser, Martin J.; Brodie, Eoin L.; Domínguez-Bello, María Gloria

doi:10.1038/ismej.2010.149

Cited by 264 publications

(244 citation statements)

References 34 publications

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“…As mice are coprophagic, these additional gastric bacteria could originate from the mouse's own fecal microbiota. The acquisition of additional gastric bacteria is consistent with the recent observation that H. pylori-infected Mongolian gerbils also acquire new gastric microbiota, including Lactobacillus spp., after colonization and that humans infected with H. pylori have marked differences in the structure of their gastric microbial community (Maldonado-Contreras et al 2011;Zaman et al 2010).…”

Section: Discussionmentioning

confidence: 99%

Helicobacter felis–Associated Gastric Disease in Microbiota-Restricted Mice

Schmitz

Durham²,

Schoeb³

et al. 2011

J Histochem Cytochem.

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SummaryHuman Helicobacter pylori infection leads to multiple pathological consequences, including gastritis and adenocarcinoma. Although this association has led to the classification of H. pylori as a type 1 carcinogen, it is not clear if additional nonhelicobacter gastric microbiota play a role in these diseases. In this study, we utilized either specific pathogen-free C57BL/6 mice (B6.SPF) or mice colonized with altered Schaedler flora (B6.ASF) to evaluate the role of nonhelicobacter gastric microbiota in disease development after Helicobacter felis infection. Despite similar histological changes, H. felis persisted in B6.ASF stomachs, while H. felis could no longer be detected in the majority of B6.SPF mice. The B6.SPF mice also acquired multiple Lactobacillus spp. in their stomachs after H. felis infection. Our data indicate that potential mechanisms responsible for the ineffective H. felis clearance in the B6.ASF model include the absence of new gastric microbiota to compete for the gastric niche, the lack of expression of new gastric mucins, and a reduced ratio of H. felis-specific IgG2c:IgG1 serum antibodies. These data suggest that although H. felis is sufficient to initiate gastric inflammation and atrophy, bacterial eradication and the systemic immune response to infection are significantly influenced by pre-existing and acquired gastric microbiota. (J Histochem Cytochem 59:826-841, 2011)

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Section: Discussionmentioning

confidence: 99%

Helicobacter felis–Associated Gastric Disease in Microbiota-Restricted Mice

Schmitz

Durham²,

Schoeb³

et al. 2011

J Histochem Cytochem.

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“…11,14 These caveats aside, cultivationindependent methods suggest that the gastric community is in fact distinct, even when H. pylori is not present. 11,[14][15][16] This conclusion is supported by both sequence abundance weighted and unweighted phylogeny-based community analyses, irrespective of H. pylori infection status or gastric anatomical site. While communities sampled from oral (dental plaque, tongue, pharynx) and gastric habitats (antrum, corpus) frequently segregate by site, there is some degree of overlap among samples, which is perhaps to be expected given the continual flow of food and saliva from the mouth to the stomach.…”

Section: Is There a Truly Distinct Autochthonous Gastricmentioning

confidence: 99%

The gastric microbial community,Helicobacter pyloricolonization, and disease

Martín

Solnick

2014

Gut Microbes

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“…These and additional environments where TM6 was detected in 16S rRNA gene clone libraries, including a number of biofilm-related samples, are highlighted in SI Appendix, Table S1. Notably, only a few TM6 sequence signatures have so far been identified as associated with a human host (51). We designate the clade that our TM6 16S fell within as TM6 clade I (Fig.…”

Section: Phylogenetic and Phylogenomic Analyses Of Candidate Phylum Tm6mentioning

confidence: 99%

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

McLean

Lombardo

Badger

et al. 2013

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

165

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The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a "mini-metagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum. (1), which is accomplished using multiple displacement amplification (MDA) (2-5) of genomic DNA to obtain sufficient template. We applied a high-throughput strategy to capture and sequence genomes of bacteria from a biofilm in a hospital sink including pathogens, such as the oral periodontal pathogen (Porphyromonas gingivalis) (6) and uncultivated members (this study). Despite the fact that a typical person spends ∼90% of their time indoors (7), our knowledge of the microbial diversity of the indoor environment has only recently begun to be explored using culture-independent methods (8, 9). Biofilms within water distribution systems in particular are thought to be diverse microbial communities and potential reservoirs of disease-causing organisms in the indoor environment. Several pathogens including Escherichia coli, Legionella pneumophila (10-13), Vibrio cholerae (14), and Helicobacter pylori (15, 16) have been detected in biofilms within water distribution systems. A recent 16S rRNA gene (abbreviated henceforth as 16S unless otherwise stated) molecular survey also revealed significant loads of Mycobacterium avium in showerhead biofilms (17). Based on these findings, indoor environments can clearly serve as significant reservoirs of pathogenic bacteria, and therefore there is great interest in investigating the rare and abundant bacterial species within biofilms in these environments.One approach to capture uncultivated bacteria is to isolate single bacterial cells by fluorescent activat...

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Structure of the human gastric bacterial community in relation to Helicobacter pylori status

Cited by 264 publications

References 34 publications

Helicobacter felis–Associated Gastric Disease in Microbiota-Restricted Mice

Helicobacter felis–Associated Gastric Disease in Microbiota-Restricted Mice

The gastric microbial community,Helicobacter pyloricolonization, and disease

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

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