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The genus Xanthomonas primarily comprises phytopathogenic species. By carrying out deep phylo-taxonogenomics, we recently reported that the genera Xylella, Stenotrophomonas, and Pseudoxanthomonas are misclassified and belong to the genus Xanthomonas. Considering the importance of Xanthomonas/Xylella as plant pathogens and to further determine the taxonomic and phylogenetic breadth of this genus, we extended our earlier study by including all the reported genera and families in the order. This investigation revealed that at least four more genera belong to the genus Xanthomonas, with a notable case being Lysobacter, after which the family and order are named. Similarly, our investigation also allowed us to reveal the expanded taxonomic breadth of the related genus Rhodanobacter. This finding of a major related genus that lacks plant pathogenic species will allow for taxonomy-based comparative studies. The phylo-taxonogenomic revelations were further supported by complete 16S rRNA-based sequence boundaries proposed for genus delineation. Accordingly, we propose a taxonomic revision of these major and closely related genera along with their constituent families within the order Lysobacteraceae (Xanthomonadaceae). The identification of a major related genus lacking plant pathogenic species will be important in investigating the origin and success of pathogenic species/lineages in the genus Xanthomonas. [ABSTRACT FROM AUTHOR]

The genus Xanthomonas primarily comprises phytopathogenic species. By carrying out deep phylo-taxonogenomics, we recently reported that the genera Xylella, Stenotrophomonas, and Pseudoxanthomonas are misclassified and belong to the genus Xanthomonas. Considering the importance of Xanthomonas/Xylella as plant pathogens and to further determine the taxonomic and phylogenetic breadth of this genus, we extended our earlier study by including all the reported genera and families in the order. This investigation revealed that at least four more genera belong to the genus Xanthomonas, with a notable case being Lysobacter, after which the family and order are named. Similarly, our investigation also allowed us to reveal the expanded taxonomic breadth of the related genus Rhodanobacter. This finding of a major related genus that lacks plant pathogenic species will allow for taxonomy-based comparative studies. The phylo-taxonogenomic revelations were further supported by complete 16S rRNA-based sequence boundaries proposed for genus delineation. Accordingly, we propose a taxonomic revision of these major and closely related genera along with their constituent families within the order Lysobacteraceae (Xanthomonadaceae). The identification of a major related genus lacking plant pathogenic species will be important in investigating the origin and success of pathogenic species/lineages in the genus Xanthomonas.

Pectobacterium cacticida (formerly Erwinia cacticida) causes soft rot disease of cactus plants. Its taxonomic status within the genus Pectobacterium remains questionable because no whole genome sequence of this species is available in public databases for reliable taxonomic analyses. Here, we present the complete genome sequence of the P. cacticida type strain CFCC 10813T (=1-12T = ATCC 49481T). P. cacticida can be classified into the genus Pectobacterium because it is on the deepest basal phylogenomic branch of the genus Pectobacterium, and its genome relatedness to other Pectobacterium species is at the border for the genus delimitation boundaries. This complete genome sequence provides the genome resource for elucidating P. cacticida pathogenicity and adaptation to plant hosts and environments. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA–DNA hybridization analysis between these two species revealed a maximum identity similarity of only 27.5%. We found phenotypical and genomic differences between strain Marseille-Q4368 and its closely related species. These findings underscore the classification of this bacterium as a distinct species. Hence, we propose the name Leucobacter manosquensis sp. nov. strain Marseille-Q4368 (=CSUR Q4368 = DSM 112403) for this newly identified bacterial species. [ABSTRACT FROM AUTHOR]

A Gram-positive facultative anaerobe, nonspore forming, and nonmotile bacterial strain M31 was isolated from faecal contaminated soil. The strain is previously reported to produce a novel antimicrobial lipopeptide and displayed probiotic properties. The strain M31 is catalase negative and fermented d -galactose, d -glucose, esculin, d -maltose, d -lactose, d -melibiose, d -raffinose, d -saccharose (weak reaction), d -xylose (weak reaction), d -ribose (weak reaction), and l -arabinose (weak reaction). The majority of fatty acids were C16:0 (53.9%), C18:0 (26.9%), and C19:0 cyclo ω8c (19.1%). The genome is 2 234 040 bp long with 38.81% guanine-cytosine (GC) content. The pairwise ortho average nucleotide identity and digital DNA-DNA hybridization values of strain M31 with its closest relative species from Limosilactobacillus reuteri clade and Lm. rudii is below the recommended cut-off of 95% and 70%, respectively. Herein, we propose Lm. walteri sp. nov. as a novel species of the genus Limosilactobacillus with M31 = MTCC 12838 = JCM 32759 = KCTC 25569. [ABSTRACT FROM AUTHOR]

Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA–DNA hybridization analysis between these two species revealed a maximum identity similarity of only 27.5%. We found phenotypical and genomic differences between strain Marseille-Q4368 and its closely related species. These findings underscore the classification of this bacterium as a distinct species. Hence, we propose the name Leucobacter manosquensis sp. nov. strain Marseille-Q4368 (=CSUR Q4368 = DSM 112403) for this newly identified bacterial species.

Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA–DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively. [ABSTRACT FROM AUTHOR]

Based on phylo-taxonogenomics criteria, we present amended descriptions for 20 pathovars to Xanthomonas citri. Incidentally, 18 were first reported from India. Seven out of twenty are classified as X. axonopodis, 12 out of 20 as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining 16 were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. This proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants. [ABSTRACT FROM AUTHOR]

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).

The Microbial Culturomics Project aiming to discover several bacterial species made it possible to isolate the strain Marseille-P4308T from a stool sample of a healthy indigenous Congolese volunteer. Strain Marseille-P4308T is a Gram-positive coccus shaped bacterium that optimally grows at 37 °C. The 16S rRNA gene sequence of the strain has a 96.2% sequence similarity to Peptostreptococcus anaerobius strain NCTC 11460T (GenBank accession number: NR_042847.1). In addition, the average nucleotide identity of strain Marseille-P4308T with its closest related species was 71.1%, which was far below the recommended threshold (>95–96%). The genome of the strain Marseille-P4308T has a length of 2.14 Mbp with G + C content of 30.4 mol%. Based on phenotypic, biochemical, genomic and phylogenetic analysis, strain Marseille-P4308T (= CSUR P4308 = CECT 9960) clearly appears to be a new species for which the name Peptostreptococcus faecalis sp. nov., is proposed.

Strain Quantibio-BCGUT is a new species from the genus Parabacteroides that was isolated from a stool sample of a 49-year-old healthy Chinese male adult. Cells are Gram-negative and obligate anerobic bacilli. Strain Quantibio-BCGUT exhibits 95.86% 16S rRNA gene sequence similarity to Parabacteroides merdae strain JCM 9497 (NR_041343.1), the phylogenetically closely related species with standing in nomenclature. Major fatty acids are C16:0, C18:0 and C19:0-IS. Quantibio-BCGUT exhibits a high level of resistance to aztreonam. Growth occurred at pH 5.5–9.0. Optimal growth was observed at 35 °C in YCFA medium in anerobic condition, no growth occurs at 25 °C or 50 °C. Strain grows in YCFA medium in the presence of 0.1%–2.0% (w/v) NaCl (optimum 1.0%). Based on the phenotypic and phylogenetic evidence, OrthoANI values and results of the biochemical tests, the new species is named Parabacteroides pekinense sp. nov., for which strain Quantibio-BCGU T (= CGMCC = QHBCGU) is proposed as the type strain.

A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain 16-SW-7, isolated from a seawater sample, was investigated in detail due to its ability to produce a unique α-galactosidase converting B red blood cells into the universal type blood cells. The phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain 16-SW-7 is a member of the Gammaproteobacteria genus Pseudoalteromonas. The closest relatives of the environmental isolate were Pseudoalteromonas distincta KMM 638T and Pseudoalteromonas paragorgicola KMM 3548T, with the plural paralogous 16S rRNA genes of 99.87–100% similarity. The strain 16-SW-7 grew with 1–10% NaCl and at 4–34°C, and hydrolyzed casein, gelatin, tyrosine, and DNA. The genomic DNA G+C content was 39.3 mol%. The prevalent fatty acids were C16:1 ω7 c , C16:0, C17:1 ω8 c , C18:1 ω7 c , C17:0, and C12:0 3-OH. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, two unidentified amino lipids, and three unidentified lipids. The major respiratory quinone was Q-8. The finished genome of the strain 16-SW-7 (GenBank assembly accession number: GCA_005877035.1) has a size of 4,531,445 bp and comprises two circular chromosomes L1 and S1, deposited in the GenBank under the accession numbers CP040558 and CP040559, respectively. The strain 16-SW-7 has the ANI values of 98.2% with KMM 638T and KMM 3548T and the DDH values of 84.4 and 83.5%, respectively, indicating clearly that the three strains belonged to a single species. According to phylogenetic evidence and similarity for the chemotaxonomic and genotypic properties, the strain 16-SW-7 (= KCTC 52772 = KMM 701) represents a novel member of the species Pseudoalteromonas distincta. Also, we have proposed to reclassify Pseudoalteromonas paragorgicola as a later heterotypic synonym of P. distincta based on the rules of priority with the emendation of the species. [ABSTRACT FROM AUTHOR]

A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain 16-SW-7, isolated from a seawater sample, was investigated in detail due to its ability to produce a unique α-galactosidase converting B red blood cells into the universal type blood cells. The phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain 16-SW-7 is a member of the Gammaproteobacteria genus Pseudoalteromonas. The closest relatives of the environmental isolate were Pseudoalteromonas distincta KMM 638T and Pseudoalteromonas paragorgicola KMM 3548T, with the plural paralogous 16S rRNA genes of 99.87–100% similarity. The strain 16-SW-7 grew with 1–10% NaCl and at 4–34°C, and hydrolyzed casein, gelatin, tyrosine, and DNA. The genomic DNA G+C content was 39.3 mol%. The prevalent fatty acids were C16:1 ω7c, C16:0, C17:1 ω8c, C18:1 ω7c, C17:0, and C12:0 3-OH. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, two unidentified amino lipids, and three unidentified lipids. The major respiratory quinone was Q-8. The finished genome of the strain 16-SW-7 (GenBank assembly accession number: GCA_005877035.1) has a size of 4,531,445 bp and comprises two circular chromosomes L1 and S1, deposited in the GenBank under the accession numbers CP040558 and CP040559, respectively. The strain 16-SW-7 has the ANI values of 98.2% with KMM 638T and KMM 3548T and the DDH values of 84.4 and 83.5%, respectively, indicating clearly that the three strains belonged to a single species. According to phylogenetic evidence and similarity for the chemotaxonomic and genotypic properties, the strain 16-SW-7 (= KCTC 52772 = KMM 701) represents a novel member of the species Pseudoalteromonas distincta. Also, we have proposed to reclassify Pseudoalteromonas paragorgicola as a later heterotypic synonym of P. distincta based on the rules of priority with the emendation of the species.

Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella , Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts. • Family Lysobacteraceae includes closely related generafrom diverse ecologies such as plant, human and environment etc. • Taxonomic ambiguities in family Lysobacteraceae needs to be addressed using whole genome-based genus demarcation approaches. • Phylogenomics depict Xylella as variant lineage sandwitched between major clades of Xanthomonas infecting monocots and dicots. • Various robust taxonogenomics parameters reveal unary nature of Xanthomonas, Stenotrophomonas, Xylella and Pseudoxanthomonas. • In light of deep phylo-taxono-genomics findings and published polyphasic data warrants reunification of these four genera as Xanthomonas. [ABSTRACT FROM AUTHOR]

Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95–96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 (= CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov. is proposed. [ABSTRACT FROM AUTHOR]

Stenotrophomonas sepilia strain SM16975 (= JCM 32102; = KCTC 62052) is a new species isolated from the blood culture of a hospitalized patient. The biochemical characterization, phenotypic criteria, phylogenomic reconstruction, and genomic analysis were carried out to differentiate it from its phylogenetic neighbours, establishing novel species status in the genus Stenotrophomonas and within Stenotrophomonas maltophilia complex (Smc).

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.

Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.

An obligately anaerobic, non-motile and Gram-positive rod bacterium, strain SW219 was isolated from ceacum of feral chickens. Based on 16S rRNA sequence analysis, the strain SW219 exhibited 97.88% similarity to Collinsella massiliensis strain GD3 strain, the closest valid species. The genome size of SW219 was 2.58 Mbp with 64.5 mol% of G+C content. The phenotypic and genotypic analysis suggested that the strain SW219 is a new species belonging to the family Coriobacteriaceae within the Actinobacteria phylum, which the name Collinsella avium sp. nov. is proposed. The type strain of Collinsella avium is SW219 (= DSM 109235T and = CCOS 1884T).

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T). [ABSTRACT FROM AUTHOR]

Strain Marseille-P3248т is a new species from the order Actinomycetales that was isolated from the urine sample of a girl aged 20 months with rotavirus gastroenteritis. It is a facultative anaerobic Gram-positive rod-shaped bacterium. Strain Marseille-P3248т exhibits 94.73% sequence similarity with Arcanobacterium pluranimalium strain M430/94/2, a phylogenetically related species with standing in nomenclature. Its genome size is 1 667 964 bp with 49.1% G + C content. Strain Marseille-P3248т (= CSURP3248) is the type strain of the new species Arcanobacterium urinimassiliense sp. nov.

Lachnoclostridium phocaeense is a new species in the genus Lachnoclostridium. Lachnoclostridium phocaeense is a Gram-positive anaerobic rod. This strain, Marseille-P3177T (CSUR = P3177) with the below described genome was isolated from the urine sample of a women after kidney transplantation. The strain genome is 3 500 754 bp long with 50.62% G + C content and consists of a single contig (GenBank accession number NZ_LT635479.1).

In 2019, by culturing a skin swab from the forehead of a 70-year-old healthy woman via the culturomics method, we isolated the new bacterial strain Marseille-Q2068T (= CSUR-Q2068). Matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family Methylobacteriaceae in the phylum Proteobacteria. We describe here its main phenotypic characteristics, genome sequence and annotation of Microvirga mediterraneensis strain Marseille-Q2068T, a new member of the Microvirga genus, which we propose as the type strain.

An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.

Two new bacterial strains, Marseille-P4126 (=CSURP4126) and Marseille-P4593 (=CSURP4593), were isolated from the vaginal sample of a French woman with vaginosis. These strains were identified and characterized using the taxonogenomics method. The findings from phylogenetic tree interpretation, phenotypic criteria and genomic analysis provided here distinctly display that Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. are new members of the genus Atopobium and Butyricimonas, respectively.

During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.

Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.

In 2019, by culturing a skin swab sample from the back of the hand of a 61-year-old healthy woman and assessing it via the culturomics method, we isolated the new bacterial strain Marseille-Q0843T (= CSUR-Q0843). Matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family in Nocardioidaceae in the phylum Actinobacteria. We describe here the main phenotypic characteristics, genome sequence and annotation of Aeromicrobium phoceense strain Marseille-Q0843T, a new member of the Aeromicrobium genus, which we propose as the type strain.

Urinicoccus timonensis gen. nov., sp. nov. strain Marseille-P3926T is a new species from the phylum Firmicutes and the family Peptoniphilaceae that was isolated from a human faeces sample. Genome was 1 978 908 bp long with a 41.1 G + C content. The closest species based on 16S ribosomal RNA was Peptoniphilus ivorii DSM 10022 with 90.8% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille- P3926T as the strain type of Urinicoccus timonensis gen. nov., sp. nov.

Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.

Strain Marseille-Q1234T is a new species from the genus Halobacillus that was isolated in 2019 from a stool sample in a healthy Malian child

Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. Megasphaera vaginalis sp. nov. strain Marseille-P4512 (= CSURP4512) and Anaerococcus vaginimassiliensis sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of Firmicutes phylum.

Strain Marseille-Q0835T is an aerobic, non-motile and non-spore-forming Gram-positive coccus isolated from the stools of a Burkinabe woman. In this report, we present its phenotypic description including MALDI-TOF mass spectrometry analysis and genome sequencing. Strain Marseille-Q0835T; 2.9768-Mb genome exhibited a 41.9 mol% G+C content and 2699 predicted genes. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-Q0835T as the type strain of Enterococcus burkinafasonensis sp. nov., a new species within the family Enterococcaceae.

Anaerococcus marasmi sp. nov. strain Marseille-P3557T is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557T was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was Anaerococcus prevotii strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557T as the type strain of Anaerococcus marasmi sp. nov., a new species within the genus Anaerococcus.

Massilistercora timonensis gen. nov., sp. nov. strain Marseille-P3756T is a new species of the phylum Firmicutes; it was isolated from the human gut microbiota and has a genome of 2 769 591 bp (51.2% G + C). The closest species based on 16S rRNA sequence was Merdimonas faecis strain BR31 with 95.2 % sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P3756T as the type strain of Massilistercora timonensis sp. nov., a new species within the genus Massilistercora.

A Gram-negative and facultative anaerobic bacterium, designated strain SN4T, was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5T, the phylogenetically closest neighbor and the type species of this genus. Anteiso-C15:0, iso-C15:0 and C16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4T from G. massiliense G5T. Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov. [ABSTRACT FROM AUTHOR]

Strain 6021061333T was isolated from the sputum of 16-year-old girl with cystic fibrosis following a pulmonary exacerbation. This bacterial strain could not be identified by our systematic MALDI-TOF mass spectrometry screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 97.83% sequence identity with Chryseobacterium kwangjuense strain KJ1R5T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. Colonies are yellow, circular and 0.5–1 mm in diameter after cultivation at 28 °C for 24 h on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 28–37 °C (optimally at 28 °C). Strain 6021061333T is Gram-negative, non-motile and strictly aerobic bacillus. It is catalase and oxidase positive. The 4,864,678 bp-long genome, composed of five contigs, has a G+C content of 38.86%. Out of the 4427 predicted genes, 4342 were protein-coding genes and 85 were RNAs. The major fatty acids are branched (13-methyl-tetradecanoic acid and 15-methyl-hexadecenoic acid). Digital DNA–DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain 6021061333T against genomes of the type strains of related species ranged between 23.60 and 50.40% and between 79.31 and 93.06%, respectively. According to our taxonogenomics results, we propose the creation of Chryseobacterium phocaeense sp. nov. that contains the type strain 6021061333T (= CSUR P2660, = CECT 9670). [ABSTRACT FROM AUTHOR]

Mobilicoccus massiliensis strain SIT2 (= CSUR P1306 = DSM 29065) is a new type strain of Mobilicoccus sp. nov. isolated from the stool of a 2-year-old Nigerian boy with kwashiorkor. M. massiliensis is Gram positive, facultatively anaerobic, nonsporulating and motile. The 3 842 438 bp long genome contains 3362 protein-coding and 49 RNA genes, including one 5S rRNA gene, one 16S rRNA gene, one 23S rRNA gene and 46 tRNA genes.

Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600T, Bacillus mediterraneensis strain Marseille-P2384T, Bacillus massilinigeriensis strain Marseille-P2366T, Bacillus tuaregi strain Marseille-P2489T and Bacillus phocaeensis strain SIT16T are each the type strain of the corresponding bacterial species. These strains, the genomes of which are described here, are facultative anaerobic Gram-positive bacilli. Here, we describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

We report the main characteristics of ‘Actinomyces provencensis’ strain SN12T sp. nov., ‘Corynebacterium bouchesdurhonense’ strain SN14T sp. nov., ‘Corynebacterium provencense’ strain SN15T sp. nov. and ‘Xanthomonas massiliensis’ strain SN8T sp. nov., which were all isolated from stool samples from obese French patients.

We report here the main characteristics of five new species ‘Urmitella timonensis’ strain Marseille-P2918T (CSUR P2918), ‘Blautia marasmi’ strain Marseille-P2377T (CSUR P2377), ‘Lachnoclostridium pacaense’ strain Marseille-P3100T (CSUR P3100), ‘Bacillus marasmi’ strain Marseille-P3556T (CSUR P3556) and ‘Anaerotruncus rubiinfantis’ strain MT15T (CSUR P2276), which were isolated recently from stool samples taken from undernourished children in Niger and Senegal using microbial culturomics.

Here we report of summary of the characteristics of ‘Collinsella phocaeensis’ strain Marseille-P3245T sp. nov., ‘Clostridium merdae’ strain Marseille-P2953T, ‘Sutterella massiliensis’ strain Marseille-P2435T sp. nov., ‘Sutturella timonensis’ strain Marseille-P3282T sp. nov., ‘Enorma phocaeensis’ Marseille-P3242T sp. nov., ‘Mailhella massiliensis’ strain Marseille-P3199T gen. nov., sp. nov., ‘Mordavella massiliensis’ strain Marseille-P3246T sp. nov. and ‘Massiliprevotella massiliensis’ strain Marseille-P2439T sp. nov. isolated from fresh stool samples of healthy French patients.

We report the main characteristics of ‘Bacillus dakarensis’ P3515T sp. nov., ‘Bacillus sinesaloumensis’ P3516T sp. nov., ‘Gracilibacillus timonensis’ P2481T sp. nov., ‘Halobacillus massiliensis’ P3554T sp. nov., ‘Lentibacillus massiliensis’ P3089T sp. nov., ‘Oceanobacillus senegalensis’ P3587T sp. nov., ‘Oceanobacillus timonensis’ P3532T sp. nov., ‘Virgibacillus dakarensis’ P3469T sp. nov. and ‘Virgibacillus marseillensis’ P3610T sp. nov., that were isolated in 2016 from salty stool samples (≥1.7% NaCl) from healthy Senegalese living at Dielmo and N’diop, two villages in Senegal.

Using the culturomics strategy, a wide range of anaerobic bacteria was discovered including Anaeromassilibacillus senegalensis strain mt9T (= CSUR P1511=DSM 102954), isolated from the gut microbiota of a 1-year-old Senegalese patient with kwashiorkor. This Gram-negative strain is a strictly anaerobic, spore-forming rod motile by a polar flagellum. The 3 511 289 bp long genome of this strain contains 3046 protein-coding and 49 RNA genes, including 45 tRNA and four rRNA genes, and exhibits a G+C content of 52.94%. Here we describe the features of this organism, together with the complete genome sequence and annotation.

Paenibacillus phocaensis sp. nov. strain mt24T (= CSUR P2238 = DSM 101777) is a Gram-negative, facultative anaerobic, spore-forming and motile bacilli. This strain was isolated from the stool sample of a healthy infant from Niger. Its genome was estimated to a size of 5 521 415 bp with a 53.54% GC content. It contains 4835 protein-coding genes and 89 RNAs, among which two were 16S rRNA genes. There were also 101 genes (2.09%) identified as ORFans.

Massilioclostridium coli strain Marseille-P2976T (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976T and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes.

Prevotella phocaeensis sp. nov. strain SN19T (= DSM 103364) is a new species isolated from the gut microbiota of patient with colitis due to Clostridium difficile. Strain SN19T is Gram-negative rod-shaped bacteria, strictly anaerobic, nonmotile and non–endospore forming. The predominance fatty acid is hexadecanoic acid. Its 16S rRNA showed a 97.70% sequence identity with its phylogenetically closest species, Prevotella oralis. The genome is 2 922 117 bp long and contains 2486 predicted genes including 56 RNA genes.