Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x

Bedree, Joseph K.; Bor, Batbileg; Cen, Lujia; Edlund, Anna; Lux, Renate; McLean, Jeffrey S.; Shi, Wenyuan; He, Xuesong

doi:10.3389/fmicb.2018.02049

Cited by 39 publications

(40 citation statements)

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“…Three BGCs were identified within CPR genomes. This was surprising, as, to our knowledge, clusters have rarely been reported in CPR genomes (24). The genome Microgenomates_ANG_786 encodes a lantipeptide, Saccharibacteria_ANG_806 encodes a terpene, and Microgenomates_ANG_785 encodes a biosynthetic gene cluster detected as a linear azole/azoline-containing peptide (LAP).…”

Section: Resultsmentioning

confidence: 92%

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Sharrar

Crits-Christoph

Méheust

et al. 2020

mBio

141

104

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Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles.

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Section: Resultsmentioning

confidence: 92%

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Sharrar

Crits-Christoph

Méheust

et al. 2020

mBio

141

104

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“…It is no longer simply thought of as a collection of bacteria in a biofilm matrix. Instead, it is now recognized as a microbial community composed of Bacteria, Archaea, bacteriophages, mammalian (eukaryotic) viruses, fungi, protozoa, and the recently described ultrasmall bacterial epibionts known as candidate phyla radiation . All members of this microbial community interact with each other and the host tissues in very complex ways.…”

Section: Future Challengesmentioning

confidence: 99%

“…These techniques have broadened our understanding of complex microbial ecosystems that reside on and in us. The human oral microbiome consists of genes from the following sources: Bacteria, Archaea, Protozoa, Fungi, bacteriophages (ie, viruses that prey on Bacteria and Archaea), mammalian viruses (ie, those that prey on eukaryotic cells), and ultrasmall (200‐500 nm) epibionts or bacterial parasites known as candidate phyla radiation . These life forms that reside in oral biofilms have coevolved with us, and we are only beginning to understand the complex interlinks and importance of these microbial communities on health and disease.…”

Section: Future Challengesmentioning

confidence: 99%

“…Culture‐independent sequencing of numerous ecosystems has revealed the presence of enormous numbers of ultrasmall (200‐500 nm) bacteria known as the candidate phyla radiation . Candidate phyla radiation bacteria have been detected in subgingival plaque from sites with and without periodontitis . Some members of the candidate phyla radiation group have been suggested as periodontal pathogens .…”

Section: Future Challengesmentioning

confidence: 99%

“…Candidate phyla radiation bacteria are epibionts or parasites on other bacteria. The only member of this group that has been cultured is Nanosynbacter lyticus (strain TM7x), which has an epibiotic‐parasitic relationship with Actinomyces odontolyticus . In most ecosystems, candidate phyla radiation bacteria are commonly found and comprise at least 15% of the domain Bacteria .…”

Section: Future Challengesmentioning

confidence: 99%

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A brief history of periodontics in the United States of America: Pioneers and thought‐leaders of the past, and current challenges

Armitage

2019

Periodontology 2000

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This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought‐leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health‐care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer‐reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host‐microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.

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Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts

Bor²,

et al. 2020

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SUMMARY The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200–300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.

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Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x

Cited by 39 publications

References 98 publications

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

A brief history of periodontics in the United States of America: Pioneers and thought‐leaders of the past, and current challenges

Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts

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