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A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, helical rod-shaped bacterium, designated AGMB01872T, was isolated from faeces of a cow deposited in the National Institute of Animal Science (Wanju, Republic of Korea). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AGMB01872T was most closely related to Succinivibrio dextrinosolvens DSM 3072T (= KCTC 25222T, 96.6 %) which belonged to the family Succinivibrionaceae . Growth was occurred at 30–40 °C (optimum, 37 °C), pH 6–7 (optimum, pH 7) and in the presence of 0.5–1.0 % (w/v) NaCl. The genomic DNA G+C content of strain AGMB01872T was 35.9 mol%. The average nucleotide identity value between strain AGMB01872T and S. dextrinosolvens DSM 3072T was 72.1 %. Cells of strain AGMB01872T utilized d-glucose, maltose, d-xylose and l-arabinose. The major fatty acids (>10 %) were C14 : 0 (23.9 %), C16 : 0 (29.4 %), summed feature 5 (10.8 %) and summed feature 10 (30.3 %). The major end-product of glucose fermentation was succinate. Based on the phenotypic, phylogenetic, biochemical, genotypic and chemotaxonomic data, AGMB01872T represents a novel species within the genus Succinivibrio , for which the name Succinivibrio feacicola sp. nov. is proposed. The type strain is AGMB01872T (= KCTC 25201T=NBRC 115007T=GDMCC 1.2573T).

A novel, strictly anaerobic, gram-negative, segmented filamentous bacterium strain AGMB03513T, was isolated from the faeces of a 5-month-old pig. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the family Lachnospiraceae, and the closest strain was Anaerostipes butyraticus. Strain AGMB03513T formed a lineage within the genus Anaerostipes and was closely related to A. butyraticus DSM 22094 T (= KCTC 15125 T, 95.8%), Anaerostipes hadrus DSM 3319 T (= KCTC 15606 T, 95.5%), Anaerostipes caccae DSM 14662 T (= KCTC 15019 T, 94.0%), and Anaerostipes rhamnosivorans DSM 26241 T (= KCTC 15316 T, 93.4%). Strain AGMB03513T grew at temperatures between 30 and 45 °C, within a pH range of 7.0–9.0, and in medium containing up to 1.5% NaCl. Cells were found to utilise d-glucose, d-mannitol, d-lactose, d-saccharose, d-maltose, d-xylose, l-arabinose, d-mannose, and d-sorbitol, and acetate was identified as the major end product of metabolism. The major components of the cellular fatty acids were C12:0, C16:0, and C18:0. In addition, the bacterium contained meso-diaminopimelic acid in the cell wall. According to the comparative analysis of the whole genome sequence, the DNA G + C content of strain AGMB03513 was 37.0 mol%. In addition, Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridisation (dDDH) values were obtained in comparisons of strain AGMB03513T with reference strains of species in the genus Anaerostipes. ANI values were found to be between 71.0 and 75.7%, AAI values between 66.6 and 73.2%, and dDDH values between 19.5 and 21.4%. All the data were below the threshold range for species determination. Based on phenotypic, phylogenetic, biochemical, chemotaxonomic, and genomic characteristics, we considered it reasonable to assign a novel species status to strain AGMB03513T, for which we propose the name Anaerostipes faecalis sp. nov. The type strain is AGMB03513T (= KCTC 25020 T = NBRC 114896 T).

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundant of potential foodborne pathogens, such as

A novel actinobacterial strain, Gram-positive, anaerobic, non-motile, and rod-shaped, designated KGMB02528T, was isolated from healthy human feces. Cells of strain KGMB02528T grew optimally at pH 7.0 and 37 °C and in the presence of 0% (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain KGMB04489T belonged to the genus Collinsella and was most closely related to Collinsella aerofaciens DSM 17552T (95.8%). The DNA G + C content was 58.0 mol%. The major cellular fatty acids (> 10%) were C16:0 DMA, C16:0 ALDE, C14:0 DMA, and C12:0. The predominant end product of fermentation was acetic acid. The cell wall peptidoglycan of strain KGMB02528T contained alanine, glutamic acid, and lysine, while diaminopimelic acid was not detected. The polar lipids were composed of two unidentified phospholipids and unidentified nine glycolipids. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain KGMB02528T represents a novel species of the genus Collinsella, for which the name Collinsella acetigenes sp. nov. is proposed. The type strain is Collinsella acetigenes KGMB02528T (= KCTC 15847T = CCUG 73987T). The description of the genus Collinsella is emended to accommodate the new species. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Collinsella acetigenes KGMB02528T is MT117838. The whole-genome shotgun BioProject number is PRJNA623694 with the accession number JABBCP000000000.

Two obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming and short rod shaped bacteria, designated KGMB07931

A Gram-stain-negative, anaerobic, non-motile, rod-shaped bacterium, designated as BGYT1T, was isolated from the feces of a cow in Andong, Republic of Korea. It was studied by using a polyphasic method to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BGYT1T formed a lineage within the genus Olsenella and was most closely related to O. umbonate KCTC 15140T (98.24%). The complete genome sequence of strain BGYT1T was 2,476,083 bp long with a G+C content of 66.9 mol%. The values for ANI (76.8%), AAI (67.26%), and dDDH (22.2%) compared to the closest related species were all below the threshold for bacterial species delineation. The strain was able to grow at pH 6.0-8.0 (optimum, pH 7.0), in the presence of 0.5-1.5% NaCl (optimum, 0.5%, w/v) and at the temperature range of 35-40°C (optimum, 35°C). The predominant fatty acids were C16:0 DMA (20.15%), C16:0 (20.15%), C18:0 (10.54%) and C18:1 cis 9 (16.99%). The polar lipid profiles contained phospholipid, glycolipid and five unidentified glycolipids. Based on its phenotypic analyses, phylogenetic and physiological characteristics, strain BGYT1T represented a novel species within the genus Olsenella, for which the name Olsenella intestinalis sp. nov. is proposed. The type strain is BGYT1T (=KCTC 25379T=GDMCC 1.3011T).

A novel Gram-stain-positive, aerobic bacterial strain, designated AK-R2A1-2T, was isolated from surface-sterilized needle leaves of an Abies koreana tree. Strain AK-R2A1-2T was closely related to Subtercola boreus K300T and Subtercola lobariae 9583bT with 97.3% and 96.7% 16S rRNA gene sequence similarities, respectively, and it formed a distinct phyletic lineage from these two strains. Growth of strain AK-R2A1-2T was observed at 4–25°C with pH 5.0–8.0. Strain AK-R2A1-2T contained menaquinone 9 (MK-9) and menaquinone 10 (MK-10) as the predominant respiratory quinones. The major cellular fatty acids were anteiso-C15:0 and summed feature 8 (C18:1ω7c or/and C18:1ω6c), and the polar lipids comprised diphosphatidylglycerol (DPG), and three unknown aminolipids (AKL2, AKL3, and AKL4). The complete genome of strain AK-R2A1-2T was sequenced to understand the genetic basis of the survival strategy of the strain in low temperatures. Multiple copies of cold-associated genes involved in cold-active chaperon, stress response, and DNA repair supported survivability of the strain at low temperatures. Finally, this strain could significantly improve rice seeding growth under low temperatures. Strain AK-R2A1-2T is concluded to represent a novel species of the genus Subtercola, and the proposed name is Subtercola endophyticus sp. nov. The type strain is AK-R2A1-2T (= KCTC 49721T = GDMCC 1.2921T).

The genus Izhakiella was established and designated as a member of the family Enterobacteriaceae in 2016. Although the taxonomical classification of most members in this family has been relatively resolved after two reclassifications in 2016 and 2017, the classification of the genus Izhakiella remains ambiguous. In this study, a polyphasic approach was used to provide evidence supporting the fact that the genus Izhakiella should no longer be considered a member of Enterobacteriaceae and proposes its reclassification into the family Erwiniaceae . The phylogenetic tree of type species in the families Enterobacteriaceae and Erwiniaceae based on the sequences of the 16S rRNA gene, rpoB housekeeping gene, and the whole-genome comprising the 92 core genes revealed that the genus Izhakiella forms a phylogenetic lineage within the family Erwiniaceae . The average nucleotide identity (ANI) value of the type species with genus Izhakiella was found to be higher for the family Erwiniaceae than that for the family Enterobacteriaceae . Notably, 12 conserved signature indels (CSIs) that are exclusively shared among the Erwiniaceae clade members were found in the type strains of the genus Izhakiella . Based on these analyses, this study suggests the reclassification of I. capsodis and I. australiensis into the family Erwiniaceae .

An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111T, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111T was closely related to Ruminococcus gauveauii CCRI-16110T (93.9 %) and Blautia stercoris GAM6-1T (93.7 %), followed by Clostridium nexile DSM 1787T (93.5 %), Blautia producta ATCC 27340T (93.4 %), Blautia hydrogenotrophica DSM 10507T (93.1 %) and Blautia coccoides ATCC 29236T (93.1 %) within the family Lachnospiraceae ( Clostridium rRNA cluster XIVa). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that KGMB01111T formed a separate branch with species in the genus Blautia . The major cellular fatty acids (>10.0 %) were C16 : 0 and C18 : 1 cis 9 dimethyl acetal (DMA), and the major polar lipids were aminophospholipids and lipids. KGMB01111T contained meso-diaminopimelic acid in cell-wall peptidoglycan. The predominant end product of fermentation produced by KGMB01111T was acetic acid. Based on the whole-genome sequence, the DNA G+C content of the isolate was 44.7 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, KGMB01111T represents a novel species within the genus Blautia for which the name Blautia faecicola sp. nov. is proposed. The type strain is KGMB01111T (=KCTC 15706T=DSM 107827T).

A novel actinobacterial strain, designated KGMB04484T, was isolated from healthy human faeces sampled in the Republic of Korea. Cells of strain KGMB04484T were strictly anaerobic, Gram-stain-positive, catalase-positive, oxidase-negative, non-motile coccobacilli and formed tiny colonies on Columbia agar with 5 % horse blood. On the basis of 16S rRNA gene sequence similarity, strain KGMB04484T was affiliated with the genus Senegalimassilia in the family Coriobacteriaceae and its closest relative was Senegalimassilia anaerobia JC110T (96.28 % sequence similarity). The DNA G+C content of strain KGMB04484T was 61.2 mol%. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and three unidentified glycolipids. The predominant cellular fatty acids (>10 %) of strain KGMB04484T were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal. Based on its phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04484T is considered to represent a novel species within the genus Senegalimassilia , for which the name Senegalimassilia faecalis sp. nov. is proposed. The type strain is KGMB04484T (=KCTC 15721T=CCUG 72347T).

A novel Gram-stain-negative and strictly anaerobic bacterial strain, designated KGMB02408T, was isolated from faeces of a healthy human in the Republic of Korea. The isolate was characterized as non-motile, non-spore-forming and rod-shaped (variable in length). The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KGMB02408T belonged to the genus Bacteroides and was most closely related to Bacteroides faecichinchillae JCM 17102T (=KCTC 15666T; 96.5 %). Based on its whole-genome sequence, the DNA G+C content of the isolate was 39.5 mol%. The average nucleotide identity value between strain KGMB02408T and related species, B. faecichinchillae JCM 17102T, was 93.8 %. The major cellular fatty acids (>10 %) of the isolate were anteiso-C15 : 0, iso-C17 : 0-OH, summed feature 11 (iso-C17 : 0-OH and/or C18 : 2 DMA) and C16 : 0. Menaquinone-8 (28.6 %) and menaquinone-10 (47.1 %) were detected as the major respiratory quinones in the isolate. The major end products of glucose fermentation produced by strain KGMB02408T were lactic acid, acetic acid and formic acid. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, strain KGMB02408T represents a novel species of the genus Bacteroides in the family Bacteroidaceae . The type strain is KGMB02408T (=KCTC 15687T=DSM 107828T).

The gut microbiota (GM) has been shown to be closely associated with the development of colorectal cancer (CRC). However, the involvement of GM is CRC has mainly been demonstrated by metagenomic profiling studies showing the compositional difference between the GM of healthy individuals and that of CRC patients and not by directly studying isolated gut microbes. Thus, to discover novel gut microbes involved in CRC, we isolated the GM from the feces of healthy individuals and evaluated its anti-CRC activity in vitro and in vivo. After GM isolation, cell-free supernatants (CFSs) were prepared from the isolated gut microorganisms to efficiently screen a large amount of the GM for anti-proliferative ability in vitro. Our results showed that the CFSs of 21 GM isolates had anti-proliferative activity against human colon cancer HCT 116 cells. Of these 21 GM isolates, GM07 was chosen for additional study because it had the highest anti-cancer activity against mouse colon cancer CT 26 cells in vitro and was further evaluated in a CT 26 allograft mouse model in vivo. GM07 was identified as Odoribacter splanchnicus through phylogenetic analysis based on 16S rRNA gene sequencing. Further investigation determined that the CFS of O. splanchnicus (OsCFS) induced anti-proliferative activity via apoptosis, but not cell cycle arrest. Moreover, GC/MS analysis suggested that the putative active molecule in OsCFS is malic acid. Finally, in the CRC mouse model, peri-tumoral injection of OsCFS significantly decreased CRC formation, compared to the control group. Altogether, these findings will provide valuable information for the discovery of potential probiotic candidates that inhibit CRC.

A novel bacterial isolate designated as strain AGMB01083T was isolated from Korean cow faeces deposited in the National Institute of Animal Science (Wanju, Republic of Korea). The bacterium is obligate anaerobic, Gram-strain-positive, and motile. Cells are straight or curved rod-shaped, flagella and spores are observed. Growth occurs between 20–40 °C (temperature optimum of 35 °C), at pH 7–9 (pH optimum of 7), and in the presence of 0.5–1.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence analysis, the strain belongs to the genus Anaerosporobacter and is most closely related to A. mobilis HY-37-4T (=KCTC5027T, similarity, 95.7 %). The DNA G+C content is 36.2 mol%, determined by the whole-genome sequence. The average nucleotide identity value between strain AGMB01083T and strain A. mobilis HY-37-4T is 75.5 %, below the interspecies identity threshold value. The major cellular fatty acids (>10 %) of strain AGMB01083T are C16 : 0, C16 : 0 dimethyl acetal (DMA), and C16 : 0 3-OH. Based on the phylogenetic, phenotypic, biochemical, chemotaxonomic, and genomic characterization, strain AGMB01083T is proposed to be a novel species, named Anaerosporobacter faecicola, in the genus Anaerosporobacter . The type strain is AGMB01083T (=KCTC 15857T=NBRC 114517T).

An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces of a 2-week-old piglet raised at the National Institute of Animal Science in Wanju, Republic of Korea. Growth of strain AGMB03916T occurred at 30–45 °C (optimum, 37 °C), at pH 6–9 (optimum, pH 8) and in the presence of 0.5–1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence analyses, strain AGMB03916T was closely related to two validly published species of the genus Phocaeicola , Phocaeicola plebeius and Phocaeicola coprocola . The 16S rRNA gene sequence similarity of strain AGMB03916T compared to P. plebeius M12T (=KCTC 5793T) and P. coprocola M16T (=KCTC 5443T) were 96.3 and 95.0 %, respectively. The genomic DNA G+C content of strain AGMB03916T was 46.4 mol%. The average nucleotide identity values between strain AGMB03916T and the reference strains were 74.9–78.5 %. Cells were able to utilize d-glucose, lactose, sucrose, maltose, salicin, aesculin hydrolysis, cellobiose and raffinose. The major end product of metabolism was acetate. The major cellular fatty acids (>10 %) of the isolate were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, C16 : 0 3-OH and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA). On the basis of the genotypic, biochemical, chemotaxonomic, phenotypic and phylogenetic data, strain AGMB03916T represents a novel species of the genus Phocaeicola , for which the name Phocaeicola faecicola sp. nov. is proposed. The type strain is AGMB03916T (=KCTC 25014T=GDMCC 1.2574T).

An obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped strain AGMB00832T was isolated from swine faeces. Phylogenetic analysis based on the 16S rRNA gene, together with the housekeeping genes, gyrB and rpoD, revealed that strain AGMB00832T belonged to the genus Faecalicatena and was most closely related to Faecalicatena orotica KCTC 15331T. In biochemical analysis, strain AGMB00832T was shown to be negative for catalase, oxidase and urease. Furthermore, the isolate was positive for β-glucosidase, β-glucuronidase, glutamic acid decarboxylase, proline arylamidase, acid phosphatase and naphthol-AS-BI-phosphohydrolase. The major cellular fatty acids (> 10%) of the isolate were C14:0, C16:0 and C18:1ω11t DMA. Based on the whole genome sequence analysis, the DNA G + C content of strain AGMB00832T was 44.2 mol%, and the genome size and numbers of rRNA and tRNA genes were 5,175,159 bp, 11 and 53, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain AGMB00832T and related strains were ≤ 77.4 and 22.5%, respectively. Furthermore, the genome analysis revealed the presence of genes for alkaline shock protein 23 and cation/proton antiporters, which may facilitate growth of strain AGMB00832T in alkaline culture condition. On the basis of polyphasic taxonomic approach, strain AGMB00832T represents a novel species within the genus Faecalicatena, for which the name Faecalicatena faecalis sp. nov. is proposed. The type strain is AGMB00832T (= KCTC 15946T = NBRC 114613T).

An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490T was isolated from swine faeces. 16S rRNA gene sequence-based phylogenetic analysis indicated that the isolate belongs to the genus Peptoniphilus and that the most closely related species is Peptoniphilus gorbachii WAL 10418T (=KCTC 5947T, 97.22 % 16S rRNA gene sequence similarity). Whole genome sequence analysis determined that the DNA G+C content of strain AGMB00490T was 31.2 mol% and moreover that the genome size and numbers of tRNA and rRNA genes were 2 129 517 bp, 34 and 10, respectively. Strain AGMB00490T was negative for oxidase and urease; positive for catalase, indole production, arginine arylamidase, leucine arylamidase, tyrosine arylamidase and histidine arylamidase; and weakly positive for phenylalanine arylamidase and glycine arylamidase. The major cellular fatty acids (>10 %) of the isolate were determined to be C16 : 0 and C18 : 1 ω9c. Strain AGMB00490T produced acetic acid as a major end product of metabolism. Accordingly, phylogenetic, physiologic and chemotaxonomic analyses revealed that strain AGMB00490T represents a novel species for which the name Peptoniphilus faecalis sp. nov. is proposed. The type strain is AGMB00490T (=KCTC 15944T=NBRC 114159T).

A novel, strictly anaerobic, gram-negative, segmented filamentous bacterium (SFB), strain AGMB03513T, was isolated from the faeces of a 5-month-old pig. Comparative analysis of 16S rRNA gene sequences indicated that strain AGMB03513T forms a lineage within the genus Anaerostipes and is most closely related to Anaerostipes butyraticus DSM 22094T (= KCTC 15125T, 95.8%), Anaerostipes hadrus DSM 3319T (= KCTC 15606T, 95.5%), Anaerostipes caccae DSM 14662T (= KCTC 15019T, 94.0%), and Anaerostipes rhamnosivorans DSM 26241T (= KCTC 15316T, 93.4%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequencing analysis revealed that its closest relatives are members of the family Lachnospiraceae and that the closest related is Anaerostipes butyraticus. Strain AGMB03513T grows at temperatures of between 30 and 45°C within a pH range of 7.0 to 9.0, and in medium containing up to 1.5% NaCl. Cells were found to utilize d-glucose, d-mannitol, d-lactose, d-saccharose, d-maltose, d-xylose, l-arabinose, d-mannose, and d-sorbitol, and acetate was identified as the major end product of metabolism. The DNA G+C content of the strain is 37.0 mol%. Average nucleotide identity (ANI) values obtained in comparisons of strain AGMB03513T with reference strains of species in the genus Anaerostipes were between 71.0% and 75.7%, which are below the ANI criterion for interspecies identity. The major components of cellular fatty acids were C12:0, C16:0, and C18:0. On the basis of phenotypic, phylogenetic, biochemical, chemotaxonomic, and genomic characteristics, we consider it reasonable to assign novel species status to strain AGMB03513T, for which we propose the name Anaerostipes faecalis sp. nov. The type strain AGMB03513T (=KCTC 25020T=NBRC 114896T).

A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions—termed coaggregation—by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. Here, we employed genome-wide transposon mutagenesis to uncover fusobacterial coaggregation factors, revealing the intertwined function of a two-component signal transduction system (TCS), named CarRS, and a lysine metabolic pathway in regulating the critical coaggregation factor RadD. Transcriptome analysis shows that CarR modulates a large regulon including radD and lysine metabolic genes, such as kamA and kamD, the expression of which are highly up-regulated in the ΔcarR mutant. Significantly, the native culture medium of ΔkamA or ΔkamD mutants builds up abundant amounts of free lysine, which blocks fusobacterial coaggregation with streptococci. Our demonstration that lysine-conjugated beads trap RadD from the membrane lysates suggests that lysine utilizes RadD as its receptor to act as a metabolic inhibitor of coaggregation. Lastly, using a mouse model of preterm birth, we show that fusobacterial virulence is significantly attenuated with the ΔkamA and ΔcarR mutants, in contrast to the enhanced virulence phenotype observed upon diminishing RadD (ΔradD or ΔcarS mutant). Evidently, F. nucleatum employs the TCS CarRS and environmental lysine to modulate RadD-mediated interspecies interaction, virulence, and nutrient acquisition to thrive in the adverse environment of oral biofilms and extraoral sites.

A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions-termed coaggregation-by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. Here, we employed genome-wide transposon mutagenesis to uncover fusobacterial coaggregation factors, revealing the intertwined function of a two-component signal transduction system (TCS), named CarRS, and a lysine metabolic pathway in regulating the critical coaggregation factor RadD. Transcriptome analysis shows that CarR modulates a large regulon including radD and lysine metabolic genes, such as kamA and kamD, the expression of which are highly up-regulated in the DeltacarR mutant. Significantly, the native culture medium of DeltakamA or DeltakamD mutants builds up abundant amounts of free lysine, which blocks fusobacterial coaggregation with streptococci. Our demonstration that lysine-conjugated beads trap RadD from the membrane lysates suggests that lysine utilizes RadD as its receptor to act as a metabolic inhibitor of coaggregation. Lastly, using a mouse model of preterm birth, we show that fusobacterial virulence is significantly attenuated with the DeltakamA and DeltacarR mutants, in contrast to the enhanced virulence phenotype observed upon diminishing RadD (DeltaradD or DeltacarS mutant). Evidently, F. nucleatum employs the TCS CarRS and environmental lysine to modulate RadD-mediated interspecies interaction, virulence, and nutrient acquisition to thrive in the adverse environment of oral biofilms and extraoral sites.

Controlled RNA degradation is a crucial process in bacterial cell biology for maintaining proper transcriptome homeostasis and adaptation to changing environments. mRNA turnover in many Gram-positive bacteria involves a specialized ribonuclease called RNase J (RnJ). To date, however, nothing is known about this process in the diphtheria-causative pathogen Corynebacterium diphtheriae, nor is known the identity of this ribonuclease in this organism. Here, we report that C. diphtheriae DIP1463 encodes a predicted RnJ homolog, comprised of a conserved N-terminal β-lactamase domain, followed by β-CASP and C-terminal domains. A recombinant protein encompassing the β-lactamase domain alone displays 5′-exoribonuclease activity, which is abolished by alanine-substitution of the conserved catalytic residues His186 and His188. Intriguingly, deletion of DIP1463/rnj in C. diphtheriae reduces bacterial growth and generates cell shape abnormality with markedly augmented cell width. Comparative RNA-seq analysis revealed that RnJ controls a large regulon encoding many factors predicted to be involved in biosynthesis, regulation, transport, and iron acquisition. One upregulated gene in the ∆rnj mutant is ftsH, coding for a membrane protease (FtsH) involved in cell division, whose overexpression in the wild-type strain also caused cell-width augmentation. Critically, the ∆rnj mutant is severely attenuated in virulence in a Caenorhabditis elegans model of infection, while the FtsH-overexpressing and toxin-less strains exhibit full virulence as the wild-type strain. Evidently, RNase J is a key ribonuclease in C. diphtheriae that post-transcriptionally influences the expression of numerous factors vital to corynebacterial cell physiology and virulence. Our findings have significant implications for basic biological processes and mechanisms of corynebacterial pathogenesis.

An obligate anaerobic, Gram-stain-positive, non-spore forming, non-motile, catalase and oxidase-negative, coccoid-shaped bacterium designated AGMB00486T was isolated from swine faeces. The optimal growth of the isolate occurred at pH 8.0 and 37 ℃. Furthermore, the growth was observed in the presence of up to 4% (w/v) NaCl but not at salinity levels higher than 5%. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AGMB00486T was a member of the genus Anaerococcus and that the isolate was most closely related to Anaerococcus vaginalis KCTC 15028T (96.7% 16S rRNA gene sequence similarity) followed by Anaerococcus hydrogenalis KCTC 15014T (96.7%) and Anaerococcus senegalensis KCTC 15435T (96.3%). Whole-genome sequence analysis determined that the DNA G+C content of strain AGMB00486T was 30.1 mol%, and the genome size, numbers of tRNA and rRNA genes were 2,268,866 bp, 47 and 8, respectively. The average nucleotide identity values between strain AGMB00486T and the three related type strains were 77.0, 77.4 and 77.2%, respectively. The major cellular fatty acids (> 10%) of strain AGMB00486T were C14:0, C16:0 and C16:0 DMA. Accordingly, these distinct phenotypic and phylogenetic properties revealed that strain AGMB00486T represents a novel species, for which the name Anaerococcus faecalis sp. nov. is proposed. The type strain is AGMB00486T (= KCTC 15945T = CCTCC AB 202009T).

A novel actinobacterial strain, Gram-positive, anaerobic, non-motile, and rod-shaped, designated KGMB02528

The genus

We demonstrated successful overexpression of porcine reproductive and respiratory syndrome virus (PRRSV)-derived GP4D and GP5D antigenic proteins in Arabidopsis. Pigs immunized with transgenic plants expressing GP4D and GP5D proteins generated both humoral and cellular immune responses to PRRSV. Porcine reproductive and respiratory syndrome virus (PRRSV) causes PRRS, the most economically significant disease affecting the swine industry worldwide. However, current commercial PRRSV vaccines (killed virus or modified live vaccines) show poor efficacy and safety due to concerns such as reversion of virus to wild type and lack of cross protection. To overcome these problems, plants are considered a promising alternative to conventional platforms and as a vehicle for large-scale production of recombinant proteins. Here, we demonstrate successful production of recombinant protein vaccine by expressing codon-optimized and transmembrane-deleted recombinant glycoproteins (GP4D and GP5D) from PRRSV in planta. We generated transgenic Arabidopsis plants expressing GP4D and GP5D proteins as candidate antigens. To examine immunogenicity, pigs were fed transgenic Arabidopsis leaves expressing the GP4D and GP5D antigens (three times at 2-week intervals) and then challenged with PRRSV at 6-week post-initial treatment. Immunized pigs showed significantly lower lung lesion scores and reduced viremia and viral loads in the lung than pigs fed Arabidopsis leaves expressing mYFP (control). Immunized pigs also had higher titers of PRRSV-specific antibodies and significantly higher levels of pro-inflammatory cytokines (TNF-α and IL-12). Furthermore, the numbers of IFN-γ+-producing cells were higher, and those of regulatory T cells were lower, in GP4D and GP5D immunized pigs than in control pigs. Thus, plant-derived GP4D and GP5D proteins provide an alternative platform for producing an effective subunit vaccine against PRRSV.

Background/Aims: South Korean soldiers are exposed to similar environmental factors. In this study, we sought to evaluate the gut microbiome of healthy young male soldiers (HYMS) and to identify the primary factors influencing the microbiome composition. Methods: We prospectively collected stool from 100 HYMS and performed next-generation sequencing of the 16S rRNA genes of fecal bacteria. Clinical data, including data relating to the diet, smoking, drinking, and exercise, were collected. Results: The relative abundances of the bacterial phyla Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria were 72.3%, 14.5%, 8.9%, and 4.0%, respectively. Fifteen species, most of which belonged to Firmicutes (87%), were detected in all examined subjects. Using cluster analysis, we found that the subjects could be divided into the two enterotypes based on the gut microbiome bacterial composition. Compared with enterotype 2 subjects, subjects classified as enterotype 1 tended to be characterized by higher frequencies of potentially harmful lifestyle habits (current smoker: 55.6% vs 36.6%, p=0.222; heavy drinker: 16.7% vs 3.7%, p=0.120; insufficient physical activity: 27.8% vs 14.6%, p=0.318). We identified a significant difference in the microbiome compositions of current and noncurrent smokers (p=0.008); the former differed from the latter mainly in a relatively lower abundance of Bifidobacterium species and a higher abundance of Negativicutes. Conclusions: A high abundance of Actinobacteria and low abundance of Bacteroidetes were the main features distinguishing the gut microbiomes of HYMS, and current smokers could be differentiated from noncurrent smokers by their lower abundance of Bifidobacterium and higher abundance of Negativicutes. (Gut Liver 2021;15:243-252)

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).

A strictly anaerobic bacterium, designated as strain KGMB-03357T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10-45°C (optimum temperature of 40°C) and a pH range of 5.1-10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17T (= KCTC 15066T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM 03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3-71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357T are C16:0, C18:0, C18∶1 cis 9, and anteiso-C15∶0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).

A novel actinobacterial strain, designated KGMB04489T, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive and short-rod-shaped. On the basis of 16S rRNA gene sequence similarity, strain KGMB04489T belonged to the genus Olsenella and was most closely related to Olsenella scatoligenes SK9K4T (94.3 %), Olsenella uli ATCC 49627T (93.5 %), Olsenella umbonata lac31T (93.4 %) and Olsenella profusa D315A-29T (93.3 %). The major end product was lactic acid. The DNA G+C content was 65.5 mol%. The major cellular fatty acids of strain KGMB04489T were C18 : 1 cis9, C18 : 1 cis9 DMA and C16 : 0. Strain KGMB04489T contained meso-diaminopimelic acid as the diamino acid in the peptidoglycan. The polar lipids consisted of an unidentified phospholipid, six unidentified glycolipids and an unidentified lipid. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04489T is considered to represent a novel species within the genus Olsenella , for which the name Olsenella faecalis sp. nov. is proposed. The type strain is KGMB04489T (=KCTC 15699T=CCUG 72345T).