Draft Genome Sequence of
            <i>Romboutsia maritimum</i>
            sp. nov. Strain CCRI-22766
            <sup>T</sup>
            , Isolated from Coastal Estuarine Mud

Maheux, Andrée F.; Boudreau, Dominique K.; Bérubé, Ève; Boissinot, Maurice; Raymond, Frédéric; Brodeur, Stéphanie; Corbeil, Jacques; Brightwell, Gale; Broda, D.M.; Omar, Rabeea F.; Bergeron, Michel G.

doi:10.1128/genomea.01044-17

Cited by 4 publications

(3 citation statements)

References 6 publications

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“…Although these findings suggest that members of the Romboutsia genus are mainly gut inhabitants, Romboutsia strains have been isolated from other environmental sources as well (2, 18, 19). The type strain of the second validly described species within the genus Romboutsia, R. lituseburensis A25K T , is not of intestinal origin, but was originally isolated from soil and humus from Côte d’Ivoire (20).…”

Section: Introductionmentioning

confidence: 90%

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Gerrritsen

Hornung

Ritari

et al. 2019

Preprint

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24Cultivation-independent surveys have shown that the recently described genus Romboutsia within the 25 family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of 26Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that 27Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the 28 human intestinal isolate Romboutsia hominis FRIFI T (DSM 28814) and the soil isolate Romboutsia 29 lituseburensis A25K T (DSM 797) were sequenced. An evaluation of the common traits of this recently 30 defined genus was done based on comparative genome analysis of the two strains together with the 31 previously elucidated genome of the type species Romboutsia ilealis CRIB T . These analyses showed 32 that the genus Romboutsia covers a broad range of metabolic capabilities with respect to 33 carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end 34 products. Main differences between strains were found in their abilities to utilize specific 35 carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. 36In addition, differences were found with respect to bile metabolism and motility-related gene clusters. 37 38

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Section: Introductionmentioning

confidence: 90%

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Gerrritsen

Hornung

Ritari

et al. 2019

Preprint

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“…Several of these other Romboutsia species ( viz . ‘ R. maritimum , ‘ R. timonensis ’ and ‘ R. weinsteinii ’) are non-validly published and there is no phenotypic/chemotaxonomic information available for them [58, 59]. However, the other validly published Romboutsia species should be presently regarded as Peptostreptococcaceae incertae sedis , pending further information which could clarify their evolutionary and taxonomic relationships.…”

Section: Discussionmentioning

confidence: 99%

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Bello,

McQuay,

Rudra

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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The family Peptostreptococcaceae, which contains 15 genera including Clostridioides, presently lacks proper circumscription. Using 52 available genomes for Peptostreptococcaceae species, we report comprehensive phylogenomic and comparative analyses to reliably discern their evolutionary relationships. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, the examined species formed a strongly supported clade designated as Peptostreptococcaceae sensu stricto. This clade encompassed the genera Peptostreptococcus (type genus), Asaccharospora, Clostridioides, Intestinibacter, Paeniclostridium, Paraclostridium, Peptacetobacter, Romboutsia and Terrisporobacter, and two misclassified species (viz. Eubacterium tenue and ‘Clostridium dakarense’). The distinctness of this clade is strongly supported by eight identified conserved signature indels (CSIs), which are specific for the species from this clade. Based on the robust evidence provided by presented studies, we are proposing the emendment of family Peptostreptococcaceae to only the genera within the Peptostreptococcaceae sensu stricto clade. We also report 67 other novel CSIs, which reliably demarcate different Peptostreptococcaceae species clades and clarify the classification of some misclassified species. Based on the consistent evidence obtained from different presented studies, we are making the following proposals to clarify the classification of Peptostreptococcaceae species: (i) transfer of Eubacterium tenue, Paeniclostridium ghonii and Paeniclostridium sordellii as comb. nov. into the genus Paraclostridium; (ii) transfer of Clostridioides mangenotii as a comb. nov. into Metaclostridioides gen. nov.; (iii) classification of ‘Clostridium dakarense’ as a novel species Faecalimicrobium dakarense gen. nov., sp. nov. (type strain FF1T; genome and 16S rRNA accession numbers GCA_000499525.1 and KC517358, respectively); (iv) transfer of two misclassified species, Clostridium paradoxum and Clostridium thermoalcaliphilum, into Alkalithermobacter gen. nov.; and (v) proposals for two novel families, Peptoclostridiaceae fam. nov. and Tepidibacteraceae fam. nov., to accommodate remaining unclassified Peptostreptococcaceae genera. The described CSIs specific for different families and genera provide novel and reliable means for the identification, diagnostics and biochemical studies on these bacteria.

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“…In contrast, Romboutsia contributed to the anaerobic phenotype of the three snails, especially in SQ and RP. The members of this genus are gram-positive and sporeforming obligate anaerobes that are present not only in human and animal guts but also in natural environments such as coastal estuarine mud and alkaline-saline lake sediment (Gerritsen et al, 2014;Wang et al, 2015;Ricaboni et al, 2016;Maheux et al, 2017).…”

Section: The Function Of Gut Microbiota In Snailsmentioning

confidence: 99%

Host species of freshwater snails within the same freshwater ecosystem shapes the intestinal microbiome

Hu,

Tong,

Chang

et al. 2024

Front. Ecol. Evol.

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BackgroundFreshwater snails are not only intermediate hosts for parasites but also an important part of the food chain as they convert plant biomass and humus into animal biomass. However, being widely distributed in freshwater environments, snails are highly affected by human activities, which makes their adaptation to altering environments challenging. The gut microbiome helps animals in their digestion, immune system, growth and adapting to changing environments. The effect of host species on intestinal microbial community has been poorly studied in snails.MethodsIn this study, single-molecule real-time sequencing technology (SMRT) was used to obtain full-length 16S rRNA genes to determine the intestinal microbiomes of three species of freshwater snails (SQ: Sinotaia quadrata, BU: Boreoelona ussuriensis, RP: Radix plicatula) with similar feeding habits in a same water environment.ResultsUnifrac PCoA (P<0.05), hierarchical cluster and Ternary analyses showed distinct and significant segregation of the intestinal microbiomes of the three hosts. The phyla Cyanobacteria, Proteobacteria, Firmicutes and Planctomycetota dominated snail guts, comprising 93.47%, 86.22%, and 94.34% of the total reads in SQ, BU and RP, respectively. Of these, only 25.26% of OTUs were identified up to species level, while 72.07% of OTUs were identified at the genus level. Although 72.94% of the total bacterial species (566) were common to three snails, significant differences were observed in terms of their abundance (P < 0.05). Several genera can help to determine the phenotype of the intestinal microbiota. In this case, Lelliottia contributed mainly to stress tolerance, biofilm formation, potential pathogenicity, mobile elements and facultatively anaerobic phenotypes in RP. Furthermore, Romboutsia and Clostridium_sensu_stricto_1 contributed to the anaerobic phenotype of SQ and RP, while Pirellula contributed to the aerobic phenotype in SQ. Moreover, PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) predicted 68 GH (glycoside hydrolase) genes, with these including monosaccharide-, disaccharide-, polysaccharide-, and starch-digesting enzyme genes as well as enzymes specific to aquatic plants. Many of the identified pathways were related to Infectious diseases and Xenobiotics biodegradation and metabolism, which expanded the resistance of freshwater snails.ConcludesLelliottia, Romboutsia, Clostridium_sensu_stricto_1, and Pirellula play an important role in the intestinal microbiota phenotype of the host snails. In general, the host species affects the structure of the gut microbial community, which in turn helps gastropods improve their environmental adaptability, but further study is still needed.

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Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766 ^T , Isolated from Coastal Estuarine Mud

Abstract: The Romboutsia maritimum sp. nov. CCRI-22766T strain was isolated from coastal estuarine mud in New Zealand. The genome assembly comprised 2,854,352 bp, with 27.1% G+C content. This is the first documentation that reports the genome sequence of R. maritimum.

Cited by 4 publications

References 6 publications

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Host species of freshwater snails within the same freshwater ecosystem shapes the intestinal microbiome

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Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766 T , Isolated from Coastal Estuarine Mud

Abstract: The Romboutsia maritimum sp. nov. CCRI-22766T strain was isolated from coastal estuarine mud in New Zealand. The genome assembly comprised 2,854,352 bp, with 27.1% G+C content. This is the first documentation that reports the genome sequence of R. maritimum.

Cited by 4 publications

References 6 publications

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

A comparative and functional genomics analysis of the genusRomboutsiaprovides insight into adaptation to an intestinal lifestyle

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Host species of freshwater snails within the same freshwater ecosystem shapes the intestinal microbiome

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Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766 ^T , Isolated from Coastal Estuarine Mud