Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo; Hunter, Ryan C.; Cheng, Genhong; Nelson, Karen E.; Lux, Renate; Shi, Wenyuan

doi:10.1073/pnas.1419038112

Cited by 416 publications

(610 citation statements)

References 43 publications

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“…Based on information available from hundreds of genomes from genome-resolved metagenomics and single-cell genomics methods to date, all members have relatively small genomes and most have somewhat (if not highly) restricted metabolic capacities 7,13,24 . Many are inferred (and some have been shown) to be symbionts 7,25,26 . Thus far, all cells lack complete citric acid cycles and respiratory chains and most have limited or no ability to synthesize nucleotides and amino acids.…”

Section: Korarchmentioning

confidence: 99%

A new view of the tree of life

et al. 2016

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The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

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Section: Korarchmentioning

confidence: 99%

A new view of the tree of life

et al. 2016

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“…The recently cultivated TM7 strain TM7x has a reduced genome of 705 kb, which lacks the genes necessary for essential amino acid biosynthesis; consequently, it is incapable of independent growth and leads an obligately symbiotic relationship with another bacterium, Actinomyces odontolyticus (He et al 2015). Davis et al (2013) also showed that gene loss in bacteria is associated with auxotrophy for purine, pyrimidine, fatty acid, and amino acid synthetic pathways.…”

Section: Introductionmentioning

confidence: 99%

First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063)

et al. 2016

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Despite significant advances in recent years in culture-independent molecular microbiology methods, the detailed study of individual bacterial species still relies on having pure cultures in the laboratory. Yet, more than a third of the approximately 700 bacterial taxa found in the human oral cavity are as yet uncultivated in vitro. One such taxon, Tannerella sp. , is the focus of much interest since it is associated with periodontal health, while Tannerella forsythia, its closest phylogenetic neighbor, is strongly associated with periodontal disease. HOT-286, however, has remained uncultivated despite the efforts of several research groups, spanning over a decade. The aim of this study was to cultivate Tannerella sp. HOT-286. A heavily diluted sample of subgingival plaque was inoculated onto culture plates supplemented with siderophores (pyoverdines-Fe complex or desferricoprogen) or a neat plaque suspension. After 8 d of anaerobic incubation, microcolonies and colonies showing satellitism were passaged onto fresh culture plates cross-streaked with potential helper strains or onto cellulose-acetate membranes placed over lawn cultures of helper strains. Subcultured colonies were identified by 16S rRNA gene sequencing, and purity was confirmed by sequencing 20 clones per library prepared from a single colony. Three colonies of interest (derived from pyoverdines-and plaque-supplemented plates) were identified as Tannerella sp. HOT-286. The isolates were found to be incapable of independent growth, requiring helpers such as Propionibacterium acnes and Prevotella intermedia for stimulation, with best growth on membranes over "helper" lawns. A representative isolate was subjected to phenotypic characterization and found to produce a range of glycosidic and proteolytic enzymes. Further comparison of this novel "periodontal health-associated" taxon with T. forsythia will be valuable in investigating virulence factors of the latter and possible health benefits of the former.

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“…The recent successful isolation of a member of the phylum TM7 by He et al (24) has shown that the relationship between oral bacteria can be more intimate, with the demonstration that the TM7 organism isolated has an intracellular lifestyle, growing within the cells of another species.…”

Section: Discussionmentioning

confidence: 99%

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

Thompson

Rybalka

Moazzez

et al. 2015

Appl Environ Microbiol

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dAround a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.T he human mouth is colonized by a diverse collection of microorganisms, including fungi, protozoa, viruses, archaea, and bacteria (1). Release 13.2 of the Human Oral Microbiome Database (www.homd.org) lists 707 taxa at the species level, of which 244 have yet to be cultured (2, 3). Oral bacteria are associated with the most common bacterial diseases of humans: dental caries and periodontal disease. In addition, they play a role in systemic disease, both directly by causing infections at other body sites and indirectly, where, for example, periodontal disease is a risk factor for other conditions such as cardiovascular disease and diabetes (4-6). Oral bacteria are also important in health; the presence of the normal microbiota inhibits infection by exogenous organisms. They also play an important role in nitrogen metabolism, whereby oral bacteria produce nitrate reductase to reduce dietary nitrate to nitrite, which is taken up the body and converted to nitric oxide, which is essential for cardiovascular health (7).The development of culture-independent methods targeting 16S rRNA genes for the characterization of complex bacterial communities has revealed the diver...

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Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

Cited by 416 publications

References 43 publications

A new view of the tree of life

A new view of the tree of life

First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063)

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

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