Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov.

Abstract

Faecalibacterium prausnitzii is one of the most important butyrate-producing bacteria in the human gut. Previous studies have suggested the presence of several phylogenetic groups, with differences at the species level, in the species, and a taxonomic re-evaluation is thus essential for further understanding of ecology of the important human symbiont. Here we examine the phenotypic, physiological, chemotaxonomic and phylogenomic characteristics of six F. prausnitzii strains (BCRC 81047T=ATCC 27768T, A2-165T=JCM 31915T, APC918/95b=JCM 39207, APC942/30−2=JCM 39208, APC924/119=JCM 39209 and APC922/41−1T=JCM 39210T) deposited in public culture collections with two reference strains of Faecalibacterium butyricigenerans JCM 39212T and Faecalibacterium longum JCM 39211T. Faecalibacterium sp. JCM 17207T isolated from caecum of broiler chicken was also included. Three strains of F. prausnitzii (BCRC 81047T, JCM 39207 and JCM 39209) shared more than 96.6 % average nucleotide identity (ANI) and 69.6 % digital DNA–DNA hybridization (dDDH) values, indicating that the three strains are members of the same species. On the other hand, the remaining three strains of F. prausnitzii (JCM 31915T, JCM 39208 and JCM 39210T) were clearly separated from the above three strains based on the ANI and dDDH values. Rather, JCM 39208 showed ANI and dDDH values over the cut-off values of species discrimination (>70 % dDDH and >95–96 % ANI) with F. longum JCM 39211T, whereas JCM 31915T, JCM 39210T and JCM 17207T did not share dDDH and ANI values over the currently accepted cut-off values with any of the tested strains, including among them. Furthermore, the cellular fatty acid patterns of these strains were slightly different from other F. prausnitzii strains. Based on the collected data, F. prausnitzii JCM 31915T, F. prausnitzii JCM 39210T and Faecalibacterium sp. JCM 17207T represent three novel species of the genus Faecalibacterium , for which the names Faecalibacterium duncaniae sp. nov. (type strain JCM 31915T=DSM 17677T=A2-165T), Faecalibacterium hattorii sp. nov. (type strain JCM 39210T=DSM 107841T=APC922/41-1T) and Faecalibacterium gallinarum sp. nov. (type strain JCM 17207T=DSM 23680T=ic1379T) are proposed.

Application of computational data modeling to a large-scale population cohort assists the discovery of specific nutrients that influence beneficial human gut bacteriaFaecalibacterium prausnitzii

“…We also observed strain specific growth response when inositol was given as a carbon source. Recently, a branch of F. prausnitzii , including A2-165 strain has been reannotated into a new species Faecalibacterium duncaniae [52], further highlighting the diverse metabolic potential of F. prausnitzii . Interestingly, it was reported that neither F. duncaniae nor F. prausnitzii grew on inositol, which contrasts with our findings.…”

Spotty liver disease adversely affect the gut microbiota of layers hen

“…When the microbiota communities of the challenged and unchallenged birds were investigated in more detail, it was observed that Faecalibacterium and Megamonas genera were reduced in the challenged groups compared to the non-challenged group. Faecalibacterium prausnitzii is the most well-characterized species of the Faecalibacterium genus, and other species have recently been identified and reported, including F. moorei ( 19 ), F. butyricigenerans, F. hominis, F. longum ( 20 ), F. duncaniae, F. gallinarum , and F. hattorii ( 21 ). Most Faecalibacterium bacteria are butyric acid producers, therefore they can exhibit anti-inflammatory effects and are potential probiotics for the treatment of gut inflammation ( 20 ).…”

Immunomagnetic Capture of Faecalibacterium prausnitzii Selectively Modifies the Fecal Microbiota and Its Immunomodulatory Profile

“…In view of these facts, increasing research has focused on this particular gut bacterium, which has been proposed as a potential next-generation probiotic ( 14 ). This has accelerated research into this bacterial group, and expanding comparative genomic investigation has led to a proposed separation of former F. prausnitzii species into different Faecalibacterium species, including F. longum , F. butyricigenerans , F. prausnitzii , F. duncaniae; F. hattorii , and F. gallinarum , together with a number of still unassigned Faecalibacterium species ( 15 – 17 ). Thus, a word of caution should be given as most literature up to the past year referred exclusively to F. prausnitzii species, while several of the strains have been recently reclassified into novel separate species.…”