Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria

Nie, Jie; Utter, Daniel R.; Kerns, Kristopher A.; Lamont, Eleanor I.; Hendrickson, Erik L.; Liu, Jett; Wu, Tingxi; He, Xuesong; McLean, Jeffrey S.; Bor, Batbileg

doi:10.1128/msystems.01488-21

Cited by 11 publications

(14 citation statements)

References 61 publications

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“…Pseudoflavonifractor is also a bacterium that can produce butyrate (Kläring et al, 2013;Sakamoto et al, 2018). At present, there are few studies on Candidatus saccharibacteria, which are directly involved in the degradation of hydrocarbons (Figueroa-Gonzalez et al, 2020;Nie et al, 2022). Similar phenomena have also been found in other plateau species.…”

Section: Discussionmentioning

confidence: 87%

Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment

Wang²,

Liu³

et al. 2023

Front. Microbiol.

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Gut microbiota not only helps the hosts to perform many key physiological functions such as food digestion, energy harvesting and immune regulation, but also influences host ecology and facilitates adaptation of the host to extreme environments. Plateau zokors epitomize successful physiological adaptation to their living environment in the face of the harsh environment characterized by low temperature, low pressure and hypoxia in the Tibetan plateau region and high concentrations of CO2 in their burrows. Therefore, here we used a metagenomic sequencing approach to explore how gut microbiota contributed to the adaptive evolution of the plateau zokor on the Qinghai-Tibet Plateau. Our metagenomic results show that the gut microbiota of plateau zokors on the Tibetan plateau is not only enriched in a large number of species related to energy metabolism and production of short-chain fatty acids (SCFAs), but also significantly enriched the KO terms that involve carbohydrate uptake pathways, which well address energy uptake in plateau zokors while also reducing inflammatory responses due to low pressure, hypoxia and high CO2 concentrations. There was also a significant enrichment of tripeptidyl-peptidase II (TPPII) associated with antigen processing, apoptosis, DNA damage repair and cell division, which may facilitate the immune response and tissue damage repair in plateau zokors under extreme conditions. These results suggest that these gut microbiota and their metabolites together contribute to the physiological adaptation of plateau zokors, providing new insights into the contribution of the microbiome to the evolution of mammalian adaptation.

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Section: Discussionmentioning

confidence: 87%

Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment

Wang²,

Liu³

et al. 2023

Front. Microbiol.

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“…HMSC075C01, A. naeslundii , and A. viscosus . These species are particularly notable as a majority of cultured Saccharibacteria attach to host bacteria from the Actinomyces genus 5,42 . One of the co-targeted Saccharibacteria phages contained numerous spacer hits from a variety of Actinobacteria species (Figure 5A).…”

Section: Resultsmentioning

confidence: 99%

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

Liu

Jaffe

Chen

et al. 2022

Preprint

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Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We sought phages that are capable of infecting these bacteria, as these may prove effective for phage therapies to control oral microbiome composition. To do this we analyzed spacer inventories from CRISPR-Cas systems that themselves could be used for phage editing. Absconditabacteria and Gracilibacteria recode the typical TGA stop codon to glycine and are infected by phages that share their host's alternate genetic code. Unexpectedly, however, other predicted phages of Gracilibacteria and Absconditabacteria do not use an alternative genetic code. Some of these phages are predicted to infect both alternatively coded CPR bacteria and the standard code host bacteria upon which the CPR bacteria depend. These phages rely on other stop codons, and thus should be capable of producing viable gene products in either bacterial host type. Interestingly, we predict that phages of Saccharibacteria can replicate in Actinobacteria, which are likely the Saccharibacteria hosts. Overall, this broad host range behavior may be advantageous for the production of CPR phage therapy agents, as non-CPR bacteria are easier to cultivate than CPR bacteria. Absconditabacteria and Gracilibacteria phages may have avoided acquisition of in-frame stop codons to increase the diversity of bacteria in which they can replicate.

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“…The nine “ Candidatus Nanosynbacter sp. HMT-352” (hereafter, HMT-352) strains reported here ( Table 1 ) were recently isolated from the human oral cavity ( 1 ) and are the first members of the phylum “ Candidatus Saccharibacteria,” a major lineage of the Candidate Phyla Radiation (CPR) ( 2 ), to be characterized at the strain level.…”

Section: Announcementmentioning

confidence: 99%

“…These nine HMT-352 strains were isolated from human saliva using a previously described “baiting” method ( 1 , 3 ). Briefly, saliva samples were centrifuged, filtered through a 0.45-μM filter, and cocultured in brain heart infusion medium (catalog number 237500; BD, NJ, USA) with potential basibionts (bacterial hosts).…”

Section: Announcementmentioning

confidence: 99%

“…The reads were quality controlled using iu-filter-quality-minoche from illumina-utils v2.12 ( 5 ). For each new HMT-352 strain, genomes were assembled using a previously described Anvi’o v7.1 workflow ( 1 , 6 ) that employed both the isolate and coculture genomic libraries. Briefly, for each strain, libraries from the isolated HMT-352 were individually assembled using metaSPAdes v3.15.3 ( 7 ) and binned using MaxBin2 v2.2.4-1 ( 8 ).…”

Section: Announcementmentioning

confidence: 99%

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Draft Genome Sequences of Nine “ Candidatus Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity

Liu¹,

Utter

Nie

et al. 2022

Microbiol Resour Announc

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Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria

Cited by 11 publications

References 61 publications

Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment

Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

Draft Genome Sequences of Nine “ Candidatus Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity

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