Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov

Abstract

<jats:p>Four strains (9CBEGH2<jats:sup>T</jats:sup>, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family <jats:italic> <jats:named-content content-type="family"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4843" xlink:type="simple">Erysipelotrichaceae</jats:ext-link> </jats:named-content> </jats:italic> and formed a monophyletic cluster with ‘<jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.35696" xlink:type="simple">Absiella argi</jats:ext-link> </jats:named-content> </jats:italic>’ strain N6H1-5 (99.4% sequence similarity) and <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4228" xlink:type="simple">Eubacterium</jats:ext-link> </jats:named-content> </jats:italic> sp. Marseille-P5640 (99.3 %). <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4246" xlink:type="simple">Eubacterium dolichum</jats:ext-link> </jats:named-content> </jats:italic> JCM 10413<jats:sup>T</jats:sup> (94.2 %) and <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4277" xlink:type="simple">Eubacterium tortuosum</jats:ext-link> </jats:named-content> </jats:italic> ATCC 25548<jats:sup>T</jats:sup> (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2<jats:sup>T</jats:sup>, ‘<jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.35696" xlink:type="simple">A. argi</jats:ext-link> </jats:named-content> </jats:italic>’ JCM 30884 and <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4228" xlink:type="simple">Eubacterium</jats:ext-link> </jats:named-content> </jats:italic> sp. Marseille-P5640 shared 98.7–99.1% average nucleotide identity (ANI) with each other. Moreover, the <jats:italic>in silico</jats:italic> DNA–DNA hybridization (DDH) values among three strains were 88.4–90.6%, indicating that these strains represent the same species. Strain 9CBEGH2<jats:sup>T</jats:sup> showed 21.5–24.1 % <jats:italic>in silico</jats:italic> DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2<jats:sup>T</jats:sup> and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for ‘<jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.35696" xlink:type="simple">A. argi</jats:ext-link> </jats:named-content> </jats:italic>’ strains identified because the name ‘<jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.35696" xlink:type="simple">A. argi</jats:ext-link> </jats:named-content> </jats:italic>’ has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2<jats:sup>T</jats:sup> represents a novel species of a novel genus, for which the name <jats:italic>Amedibacterium intestinale</jats:italic> gen. nov., sp. nov. is proposed. The type strain of <jats:italic>A. intestinale</jats:italic> is 9CBEGH2<jats:sup>T</jats:sup> (=JCM 33778<jats:sup>T</jats:sup>=DSM 110575<jats:sup>T</jats:sup>).</jats:p>

Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces

“…Differential characteristics between NSJ-176 T and type strains of closely related taxa Strains: 1, NSJ-176 T (data from this study); 2, Amedibacillus dolichus VPI C9-20 T[24]; 3, Amedibacterium intestinale 9CBEGH2 T[24]; +, Positive; -, negative; R: resistant; S: susceptible; w, weak reactions were observed. All strains listed do not have a flagellum and are non-motile, positive for acid phosphatase and negative for α-glucosidase, and all of them are susceptible to ciprofloxacin.…”

“…At the time of writing, the genus Paraeggerthella is composed of the only the type species, Paraeggerthella hongkongensis , cells of which are obligately anaerobic, non-spore-forming, Gram-stain-positive coccobacilli arranged in chains, and cells of this species metabolize 3-methyl d -glucose, palatinose, urocanic acid, l -methionine, l -threonine, l -valine, l -valine plus l -aspartic acid, uridine 5′-monophosphate and rhamnose [22, 23]. The genus Amedibacillus is composed of only one species, Amedibacillus dolichus , and the cells are Gram-stain-positive, non-spore-forming, non-motile, non-pigmented obligate anaerobic straight rods that form long chains, and the end products from metabolism of d -glucose are lactate and butyrate [24].…”

Copranaerobaculum intestinale gen. nov., sp. nov., a novel anaerobic bacterium isolated from human faeces

“… *a–h, Data from [3, 8, 11, 12, 49–52]. †DPG, diphosphatidylglycerol; PG, phosphatidylglycerol; GL, glycolipid; PGL, phenolic glycolipid; GL, glycolipid; PL, phospholipid. ‡Summed feature 3: C 16 : 1 ω 7 c and/or C 16 : 1 ω 6 c , the retention times of the two components are very similar and we cannot distinguish between them according to the standard protocol of the Microbial Identification System. …”

“…The family Erysipelotrichaceae, proposed by Verbarg et al [1], now comprises 25 genera (https://lpsn.dsmz.de/family/erysipelotrichaceae). The species listed in the family Erysipelotrichaceae are generally characterized to be Gram-stain-variable, non-sporeforming, rod-shaped, straight or slightly curved, or irregularly shaped, facultatively anaerobic, anaerobic or microaerophilic, and catalase-negative [2][3][4][5][6][7][8][9][10][11][12][13][14]. Most of the species in the family Erysipelotrichaceae can be isolated from human and animal intestine, such as canine faeces [2,3], pig intestine [4][5][6], murine intestine [7][8][9], chicken caecum [10] and human excrement [11][12][13][14].…”

“…The species listed in the family Erysipelotrichaceae are generally characterized to be Gram-stain-variable, non-sporeforming, rod-shaped, straight or slightly curved, or irregularly shaped, facultatively anaerobic, anaerobic or microaerophilic, and catalase-negative [2][3][4][5][6][7][8][9][10][11][12][13][14]. Most of the species in the family Erysipelotrichaceae can be isolated from human and animal intestine, such as canine faeces [2,3], pig intestine [4][5][6], murine intestine [7][8][9], chicken caecum [10] and human excrement [11][12][13][14]. Presently, the bacteria of family Erysipelotrichaceae have been reported to be enriched in colorectal cancer, associated with inflammation-related disorders of the gastrointestinal tract and lipid metabolism in humans [15].…”