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

McLean, Jeffrey S.; Bor, Batbileg; Kerns, Kristopher A.; Liu, Quanhui; To, Thao T.; Solden, Lindsey; Hendrickson, Erik L.; Wrighton, Kelly; Shi, Wenyuan; He, Xuesong

doi:10.1016/j.celrep.2020.107939

Cited by 165 publications

(142 citation statements)

References 62 publications

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“…Comparative genomics revealed both cell surface and intracellular proteins that are differentially enriched in susceptible vs. resistant and permissive vs. nonpermissive strains ( Table 1). Our previous transcriptomic analysis and recent study based on predicted metabolic complementarity between TM7x and XH001 similarly identified the importance of cell surface and cell wall components in the TM7x/ XH001 relationship [38,55]. Consistent with this idea, our analysis showed that most of the groups were enriched with different cell wall modifying genes at the carbohydrate and peptidoglycan modules (Table 1).…”

Section: Discussionsupporting

confidence: 84%

“…Further, the relationships between Saccharibacteria and Actinobacteria in their native oral habitats require direct investigation. While microscopy confirms the epibiotic association is conserved [ 32 , 55 , 56 ], the potentially diverse in situ interactions could significantly alter the host/symbiont relationships. As the majority of the diverse and ubiquitous CPR phyla are thought to engage in similarly obligate symbioses [ 63 , 64 ], the extent of host range for CPR organisms could have tremendous impact on our understanding of the role such bacteria/bacteria associations play in their respective environments, from the oral microbiome to aquatic and terrestrial habitats.…”

Section: Discussionmentioning

confidence: 99%

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The saccharibacterium TM7x elicits differential responses across its host range

Utter

Cavanaugh

et al. 2020

The ISME Journal

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Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into “permissive” and “nonpermissive” based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

The saccharibacterium TM7x elicits differential responses across its host range

Utter

Cavanaugh

et al. 2020

The ISME Journal

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“…Portnoybacteria bacterium BS750m-G76. These proteins were unique for these microbes in the entire euxinic waters, which suggests a parasitic lifestyle from which these Patescibacteria could translocate nutrients, proteins, and DNA from or to a putative host [22].…”

Section: Resultsmentioning

confidence: 99%

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

Cabello‐Yeves

Callieri

Picazo

et al. 2020

Preprint

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Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of 'dark matter' streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

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“…16S rRNA gene sequencing revealed several samples with enriched growth of Saccharibacteria phylum G3 group member HMT‐351, provisionally named “Ca. Nanosyncoccus nanoralicus” (McLean et al., 2018, 2020), that is likely an epibiont parasite on a bacterial host similar to strain TM7x (He et al., 2015). To identify the potential host of this bacterium, samples were divided into a group of biofilms with G3 HMT‐351 present and a group with G3 HMT‐351 absent, and the relative abundance of each species was averaged within each group.…”

Section: Methodsmentioning

confidence: 99%

Modified SHI medium supports growth of a disease‐state subgingival polymicrobial community in vitro

Lamont

Gadkari

Kerns

et al. 2020

Molecular Oral Microbiology

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Developing a laboratory model of oral polymicrobial communities is essential for in vitro studies of the transition from healthy to diseased oral plaque. SHI medium is an enriched growth medium capable of supporting in vitro biofilms with similar diversity to healthy supragingival inocula; however, this medium does not maintain the diversity of gram‐negative bacteria more associated with subgingival plaque. Here, we systematically modified SHI medium components to investigate the impacts of varying nutrients and develop a medium capable of supporting a specific disease‐state subgingival community. A diseased subgingival plaque sample was inoculated in SHI medium with increasing concentrations of sucrose (0%, 0.1%, 0.5%), fetal bovine serum (FBS) (0%, 10%, 20%, 30%, 50%), and mucin (0.1, 2.5, 8.0 g/L) and grown for 48 hrs, then the 16S rRNA profiles of the resulting biofilms were examined. In total, these conditions were able to capture 89 of the 119 species and 43 of the 51 genera found in the subgingival inoculum. Interestingly, biofilms grown in high sucrose media, although dominated by acidogenic Firmicutes with a low final pH, contained several uncultured taxa from the genus Treponema, information that may aid culturing these periodontitis‐associated fastidious organisms. Biofilms grown in a modified medium (here named subSHI‐v1 medium) with 0.1% sucrose and 10% FBS had a high diversity closest to the inoculum and maintained greater proportions of many gram‐negative species of interest from the subgingival periodontal pocket (including members of the genera Prevotella and Treponema, and the Candidate Phyla Radiation phylum Saccharibacteria), and therefore best represented the disease community.

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

Cited by 165 publications

References 62 publications

The saccharibacterium TM7x elicits differential responses across its host range

The saccharibacterium TM7x elicits differential responses across its host range

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

Modified SHI medium supports growth of a disease‐state subgingival polymicrobial community in vitro

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