Adlercreutzia hattorii sp. nov., an equol non-producing bacterium isolated from human faeces

Two obligately anaerobic, Gram-stain-positive, rod-shaped bacteria were isolated from faecal samples of healthy humans in Japan. 16S rRNA gene sequence analysis indicated that these two strains (8CFCBH1^T and 9CBH6) belonged to the genus Adlercreutzia, which is known as an equol-producing bacterium. The closest neighbours of strain 8CFCBH1^T were Adlercreutzia equolifaciens subsp. equolifaciens DSM 19450^T (98.6%), Adlercreutzia equolifaciens subsp. celatus do03^T (98.4%), Adlercreutzia muris WCA-131-CoC-2^T (96.6%), Parvibacter caecicola NR06^T (96.4%), Adlercreutzia caecimuris B7^T (95.3%) and Adlercreutzia mucosicola Mt1B8^T (95.3%). The closest relatives to strain 9CBH6 were A. equolifaciens subsp. equolifaciens DSM 19450^T (99.8%), A. equolifaciens subsp. celatus do03^T (99.6%) and A. muris WCA-131-CoC-2^T (96.8%). Strain 8CFCBH1^T showed 22.3-53.5% digital DNA-DNA hybridization (dDDH) values with its related species. In addition, the average nucleotide identity (ANI) values between strain 8CFCBH1^T and its related species ranged from 75.4 to 93.3%. On the other hand, strain 9CBH6 was considered as A. equolifaciens based on the dDDH and ANI values (>70% dDDH and >95-96% ANI). Strain 9CBH6 showed daidzein-converting activity, as expected from the result of genome analysis. The genome of strain 8CFCBH1^T lacked four genes involved in equol production. Growing cells of strain 8CFCBH1^T were not capable of converting daidzein. Based on the collected data, strain 8CFCBH1^T represents a novel species in the genus Adlercreutzia, for which the name Adlercreutzia hattorii sp. nov. is proposed. The type strain of A. hattorii is 8CFCBH1^T (=JCM 34083^T=DSM 112284^T).

Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces

An obligately anaerobic, Gram-stain-negative, rod-shaped bacterium, designated strain 2CBH44^T , was isolated from the fecal sample of a healthy Japanese man. This strain was initially assigned as a novel species of the genus Coprobacter based on the 16S rRNA gene sequence similarities compared with other Coprobacter species. The 16S rRNA gene sequence analysis revealed strain 2CBH44^T had relatively low 16S rRNA gene sequence similarity (97.5%) to Coprobacter secundus 177^T . However, strain 2CBH44^T showed 96.9% average nucleotide identity value with C. secundus 177^T , indicating that strain 2CBH44^T and C. secundus 177^T belong to the same species. On the other hand, the digital DNA-DNA hybridization value between strain 2CBH44^T and C. secundus 177^T was 73.5%, indicating that strain 2CBH44^T is a subspecies of C. secundus. Another anaerobic, Gram-stain-variable, rod-shaped bacterium, designated strain 12CBH8^T , was also isolated from human feces. Strain 12CBH8^T had significantly low 16S rRNA gene sequence similarities (<92.0%) to the validated bacterial species within the family Oscillospiraceae. The percentage of conserved protein values between the genome of strain 12CBH8^T and that of the validated related taxa were <50%, suggesting that strain 12CBH8^T belongs to a novel genus. On the basis of the collected data, strain 2CBH44^T represents a novel subspecies of C. secundus, for which the name Coprobacter secundus subsp. similis subsp. nov. (type strain 2CBH44^T  = JCM 34079^T  = DSM 111570^T ) is proposed. Strain 12CBH8^T represents a novel species of a novel genus, for which the name Solibaculum mannosilyticum gen. nov., sp. nov. (type strain 12CBH8^T  = JCM 34081^T  = DSM 111571^T ) is proposed.

Fecal Microbiota Perspective for Evaluation of Prebiotic Potential of Bamboo Hemicellulose Hydrolysate in Mice: A Preliminary Study

Bamboo hemicellulose hydrolysate (BHH) may possess antihypercholesterolemic activity; however, this activity requires further comprehensive study to assess the prebiotic mechanisms of BHH in vivo. Here, we used high-throughput 16S rRNA gene sequencing to preliminarily investigate the correlations between BHH and the fecal microbiomes of three groups of mice fed either a normal diet, a high-fat diet, or a high-fat diet supplemented with 5% BHH for 5 weeks. Alpha diversity (within community) was nonsignificant for all groups; however, beta diversity analysis among communities showed that 5% BHH suppressed the significant changes induced by the high-fat diet. The Firmicutes/Bacteroidetes ratio, the family S24-7 within the order Bacteroidales, the family Lachnospiraceae and several cellulolytic taxa were slightly ameliorated in the BHH group. These results indicated that BHH supplementation influenced the gut bacterial community and suppressed the high-fat diet-induced alterations. Additionally, BHH significantly lowered the serum cholesterol levels and fecal pH. Improving short-chain fatty acid production for all of the bacterial communities in the mouse guts may induce this effect. Thus, the prebiotic potential of BHH should be evaluated considering the gut microbial communities and their interactions.

Stress Response of Mesosutterella multiformis Mediated by Nitrate Reduction

Bacterial stress responses are closely associated with the survival and colonization of anaerobes in the human gut. Mesosutterella multiformis JCM 32464^T is a novel member of the family Sutterellaceae, an asaccharolytic bacterium. We previously demonstrated energy generation via heme biosynthesis, which is coupled with nitrate reductase. Here, physiological and morphological changes in M. multiformis induced by exposure to nitrate were investigated. The ability of M. multiformis to reduce nitrate was determined using a colorimetric assay. A unique morphology was observed during nitrate reduction under anaerobic conditions. The association between nitrate concentration and cell size or cellular fatty acid composition was evaluated. Nitrate-induced responses of M. multiformis were compared to those of related species. An increase in cellular filamentation and the ratio of saturated: unsaturated fatty acids was mediated specifically by nitrate. This indicates a decrease in cell fluidity and low leakage. Furthermore, a similar response was not observed in other related species cultured in the presence of nitrate. Hence, the nitrate-induced stress response in new anaerobes such as M. multiformis was demonstrated. The response could also be involved in the conservation of menaquinones and the maximization of nitrate reduction.

Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron

A large variety of microbes are present in the human gut, some of which are considered to interact with each other. Most of these interactions involve bacterial metabolites. Phascolarctobacterium faecium hardly uses carbohydrates for growth and instead uses succinate as a substrate. This study investigated the growth behavior of the co‐culture of the succinate‐specific utilizer P. faecium and the succinogenic gut commensal Bacteroides thetaiotaomicron. Succinate production by B. thetaiotaomicron supported the growth of P. faecium and concomitant propionate production via the succinate pathway. The succinate produced was completely converted to propionate. This result was comparable with the monoculture of P. faecium in the medium supplemented with 1% (w/v) succinate. We analyzed the transcriptional response (RNA‐Seq) between the mono‐ and co‐culture of P. faecium and B. thetaiotaomicron. Comparison of the expression levels of genes of P. faecium between the mono‐ and co‐cultured conditions highlighted that the genes putatively involved in the transportation of succinate were notably expressed under the co‐cultured conditions. Differential expression analysis showed that the presence of P. faecium induced changes in the B. thetaiotaomicron transcriptional pattern, for example, expression changes in the genes for vitamin B₁₂ transporters and reduced expression of glutamate‐dependent acid resistance system‐related genes. Also, transcriptome analysis of P. faecium suggested that glutamate and succinate might be used as sources of succinyl‐CoA, an intermediate in the succinate pathway. This study revealed some survival strategies of asaccharolytic bacteria, such as Phascolarctobacterium spp., in the human gut.

Prevotella hominis sp. nov., isolated from human faeces

A strictly anaerobic predominant bacterium, designated as strain gm001^T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001^T was identified as a member of the genus Prevotella, and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri. Phylogenomic tree analysis indicated that the gm001^T cluster is an independent lineage of P. copri DSM 18205^T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001^T and P. copri DSM 18205^T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C_15 : 0, C_15 : 0 and iso-C_15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001^T represents a novel species of the genus Prevotella, for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001^T (=BCRC 81118^T=JCM 33280^T).

Lactococcus insecticola sp. nov. and Lactococcus hodotermopsidis sp. nov., isolated from the gut of the wood-feeding lower termite Hodotermopsis sjostedti

Two strains of lactic acid bacteria, designated Hs20B0-1^T and Hs30E4-3^T, were isolated from the gut of the damp-wood termite Hodotermopsis sjostedti. These strains were characterized genetically and phenotypically. Strain Hs20B0-1^T was related to Lactococcus piscium DSM 6634^T showing 96.3 and 84.2 % sequence similarity in 16S rRNA gene and rpoB gene sequences, respectively. Strain Hs30E4-3^T was related to Lactococcus plantarum DSM 20686^T showing 94.8 and 82.2 % sequence similarity in 16S rRNA gene and rpoB gene sequences, respectively. The 16S rRNA gene sequence similarity between strains Hs20B0-1^T and Hs30E4-3^T was 95.7 %. Furthermore, genomic comparisons using pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (DDH) analyses between strain Hs20B0-1^T and L. piscium DSM 6634^T resulted in values of 73.5 and 20.1 %, respectively. Strain Hs30E4-3^T had 72.8 % ANI similarity and 21.3 % DDH similarity to L. plantarum DSM 20686^T. Strains Hs20B0-1^T and Hs30E4-3^T had 75.4 % ANI similarity and 21.1 % DDH similarity to each other. The cell-wall peptidoglycan types of strains Hs20B0-1^T and Hs30E4-3^T were A4α, Lys-Asp and A3α, Lys-Thr-Ala, respectively. The two strains, Hs20B0-1^T and Hs30E4-3^T, are distinguishable from each other and other established Lactococcus species phylogenetically and phenotypically. In conclusion, two novel species of the genus Lactococcus are proposed, namely Lactococcus insecticola Hs20B0-1^T (=JCM 33485^T=DSM 110147^T) and Lactococcus hodotermopsidis Hs30E4-3^T (=JCM 33486^T=DSM 110148^T), respectively.

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

Four strains (9CBEGH2^T, 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 Erysipelotrichaceae and formed a monophyletic cluster with 'Absiella argi' strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413^T (94.2 %) and Eubacterium tortuosum ATCC 25548^T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2^T, 'A. argi' JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7-99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA-DNA hybridization (DDH) values among three strains were 88.4-90.6%, indicating that these strains represent the same species. Strain 9CBEGH2^T showed 21.5-24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2^T 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 'A. argi' strains identified because the name 'A. argi' has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2^T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2^T (=JCM 33778^T=DSM 110575^T).

Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov

Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus Alistipes belonging to the family Rikenellaceae in the phylum Bacteroidetes, were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24^T and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to 'Alistipes obesi' ph8^T (99.73 %). Group II (strain 5CPEGH6^T) was related to Alistipes shahii WAL 8301^T (96.82 %). Ten strains of group III (3BBH6^T, 5CPYCFAH4, 5NYCFAH2 and others) were related to Alistipes onderdonkii DSM 19147^T (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6^T could be differentiated from A. shahii JCM 16773^T by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of A. onderdonkii JCM 16771^T. Strains 5CBH24^T, 6CPBBH3 and 'A. obesi' ph8^T shared 98.8-98.9 % average nucleotide identity (ANI) with each other. In addition, the in silico DNA-DNA hybridization (DDH) values among three strains were 86.7-89.4 %. Strain 5CPEGH6^T showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6^T, 5CPYCFAH4 and 5NYCFAH2) shared 97.9-99.9% ANI with each other. These three strains showed 96.9-97.3 % ANI with A. onderdonkii DSM 19147^T. The DDH values of strains 3BBH6^T, 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5-99.8 %, while those compared to A. onderdonkii DSM 19147^T were 71.0-73.4 %. On the basis of the collected data, three novel species, Alistipes communis sp. nov. (5CBH24^T=JCM 32850^T=DSM 108979^T), Alistipes dispar sp. nov. (5CPEGH6^T=JCM 32848^T=DSM 108978^T) and Alistipes onderdonkii subsp. vulgaris subsp. nov. (3BBH6^T=JCM 32839^T=DSM 108977^T), are proposed.

Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov

Previous analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related Olsenella species. To clarify the relationship of these two species, we determined the genome sequence of P. catena JCM 31932T and compared it with that already sequenced for L. massiliensis Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between P. catena JCM 31932T and L. massiliensis Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that P. catena JCM 31932T and L. massiliensis Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between L. massiliensis Marseille-P3237T and other closely related species. In addition, the genome of P. catena JCM 31932T had a high degree of synteny conservation with that of L. massiliensis Marseille-P3237T. On the basis of these findings, we propose that L. massiliensis should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).

Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megalosphaeroides sp. nov., isolated from human faeces

Two novel, obligately anaerobic, Gram-stain-negative, rod or coccoid-shaped bacteria, designated strains 4NBBH2^T and 6FBBBH3^T, were isolated from faecal samples of a healthy Japanese woman and man. The 16S rRNA gene sequence analysis showed that these strains represent a distinct lineage within the family Sutterellaceae. Strain 4NBBH2^T formed a monophyletic branch between the genera Parasutterella and Sutterella, with sequence similarity to Sutterella stercoricanis CCUG 47620^T (92.6 %), followed by Sutterella wadsworthensis WAL 7877 (92.4 %), Sutterella parvirubra YIT 11816^T (92.1 %) and Parasutterella secunda YIT 12071^T (91.8 %). Strain 6FBBBH3^T was affiliated to the genus Sutterella, with highest similarity to S. stercoricanis CCUG 47620^T (97.1 %), followed by S. parvirubra YIT 11816^T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). Strains 4NBBH2^T and 6FBBBH3^T were asaccharolytic. Analysis of fatty acids revealed that strain 4NBBH2^T could be differentiated from Sutterella species (including strain 6FBBBH3^T) by the presence of a low concentration of C16 : 1ω7c. The major respiratory quinones of strain 4NBBH2^T were menaquinone (MK)-6 and methylmenaquinone (MMK)-6, whereas those of strain 6FBBBH3^T were MK-5 and MMK-5. The G+C content of the genomic DNA of strains 4NBBH2^T and 6FBBBH3^T were 56.9 and 62.8 mol%, respectively. On the basis of the collected data, strain 4NBBH2^T represents a novel species in a novel genus of the family Sutterellaceae, for which the name Mesosutterella multiformis gen. nov., sp. nov. is proposed. The type strain is 4NBBH2^T (=JCM 32464^T=DSM 106860^T). We also propose a novel Sutterella species, Sutterellamegalosphaeroides sp. nov., for strain 6FBBBH3^T (=JCM 32470^T=DSM 106861^T).