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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).

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.

Bartonella saheliensis strain 077 (= CSUR B644T; = DSM 28003T) is a new bacterial species isolated from blood of the rodent Gerbilliscus gambianus captured in the Sine-Saloum region of Senegal. In this work we describe the characteristics of this microorganism, as well as the complete sequence of the genome and its annotation. Its genome has 2 327 299 bp (G+C content 38.4%) and codes for 2015 proteins and 53 RNA genes.

Anaerosphaera massiliensis strain Marseille-P4592T (= CSURP4592T; = CCUG72452T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo. Keywords: Anaerosphaera massiliensis, culturomics, new species, stool, taxono-genomics

A polyphasic taxono-genomic strategy was used to describe a new bacterium, strain Marseille-P1935; isolated from the gut of a healthy infant. 16S rRNA sequencing showed that the isolate belongs to the genus Haloimpatiens in the family Clostridiaceae. Phenotypic analysis and whole-genome sequence analyses confirm the status of the new species. We propose the creation of the new species Haloimpatiens massiliensis strain Marseille-P1935T (= CSURP1935T; = DSM100591T). Keywords: Culturomics, Haloimpatiens massiliensis, taxono-genomics

Bartonella massiliensis sp. nov., strain OS09T (= CSURB624T = DSM 23169), is the type strain of Bartonella massiliensis sp. nov., a new species within the genus Bartonella. It was isolated from a soft tick, Ornithodoros sonrai, vector of recurrent fever collected from Senegalese domestic rodent burrows. This strain is an aerobic, rod-shaped and Gram-negative bacterium. On the basis of taxonogenomic approach, we propose the creation of Bartonella massiliensis sp. nov. Keywords: Bartonella massiliensissp. nov., genome, Ornithodoros sonrai, senegal, soft tick

Prevotella ihumii strain Marseille-P3385T (= CSURP3385T; = DSM106428T) is a new species isolated from a fresh stool specimen of a healthy woman. Keywords: Culturomics, Prevotella ihumii, taxono-genomics

Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens. Keywords: Alistipes megaguti, Alistipes provencensis, Corynebacterium pacaense, culturomics, taxonogenomics

Dorea phocaeensis strain Marseille-P4003T (= CSURP4003T; = CCUG71359T) is a new species isolated from the stool of a healthy 29-year-old male from France. Keywords: Culturomics, Dorea phocaeensis, taxono-genomics

Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen. Keywords: Culturomics, Enterobacter timonensis, Human gut, New species, Taxonogenomics

Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo. Keywords: Culturomics, Enterococcus mediterraneensis, taxono-genomics

Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis

Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen. Keywords: Acidaminococcus provencensis, Culturomics, Microbiota, New species, Taxonogenomics, TM4000, Stool

Selenomonas felix strain Marseille-P3560T (=CSURP3560) is a new species isolated from human sputum. Keywords: Culturomics, new species, Selenomonas felix, sputum, taxonogenomics

Brachybacterium timonense strain Marseille-P4339T (=CSURP4339, =CECT9821) is a new species isolated from human sputum. Keywords: Brachybacterium timonense, culturomics, new species, sputum, taxonogenomics

Virgibacillus ndiopensis strain Marseille-P3835T (= CSURP3835T; = CCUG70388T) is a new specie isolated from the stool of a healthy 11-year-old boy from N'Diop, Senegal. Keywords: Culturomics, taxonogenomics, Virgibacillus ndiopensis

Alterileibacterium massiliense gen. nov. sp. nov. strain Marseille-P3115T (= CSURP-3115; DSM 103486), formerly proposed as Ileibacterium massiliense, is a new genus of bacteria isolated from the ileum of a human patient with Crohn's disease. Keywords: Alterileibacterium massiliense, Culturomics, Taxono-genomics

Background: A variety of natural and synthetic agents have recently been used in clinical trials to arrest dentin caries., Objectives: The aim of the present study was to explore the remineralization and antibacterial effect of natural (propolis, hesperidin) vs. synthetic (silver diamine fluoride (SDF)) agents on deep carious dentin., Material and Methods: A total of 64 human molar teeth with Class I caries were randomly distributed into 4 groups: control group; propolis group; hesperidin group; and SDF group. The cavities were prepared using the stepwise caries removal technique, and then covered with the materials to be tested. The samples were taken from the carious lesions before and after treatment to evaluate the antibacterial effect. Then, the teeth were restored with a glass ionomer cement (GIC). Digital X-rays were taken to assess remineralization and the antibacterial effect after 6 and 12 weeks., Results: The highest value of radiodensity was observed in the propolis group (46.44 ±9.65 HU), while the lowest value was noted in the hesperidin group (12.62 ±5.86 HU). The bacterial count in the propolis group was 1,280.00 ±1,480.54 CFU/mL at baseline, which was not significantly higher than the value measured after 6 weeks (574.00 ±642.48 CFU/mL; p = 0.153), whereas in the hesperidin group, the mean value of the bacterial count at baseline (3,166.67 ±1,940.79) was not much higher as compared to the value obtained at 6 weeks (2,983.33 ±1,705.77) (p = 0.150)., Conclusions: In comparison with SDF, propolis and hesperidin agents showed promising effects in terms of remineralization of carious dental tissue and hindering the progression of caries.

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis able to cause large outbreaks. The disease is polymorphic. Symptomatic primary infection is named acute Q fever and is associated with hepatitis, pneumonia, fever, and auto-immune complications while persistent focalized infections, mainly endocarditis, and vascular infections, occur in a minority of patients but are potentially lethal. In order to evaluate the genomic features, genetic diversity, evolution, as well as genetic determinants of antibiotic resistance, pathogenicity, and ability to cause outbreaks of Q fever, we performed a pangenomic analysis and genomic comparison of 75 C. burnetii strains including 63 newly sequenced genomes. Our analysis demonstrated that C. burnetii has an open pangenome, unique genes being found in many strains. In addition, pathogenicity islands were detected in all genomes. In consequence C. burnetii has a high genomic plasticity, higher than that of other intracellular bacteria. The core- and pan-genomes are made of 1,211 and 4,501 genes, respectively (ratio 0.27). The core gene-based phylogenetic analysis matched that obtained from multi-spacer typing and the distribution of plasmid types. Genomic characteristics were associated to clinical and epidemiological features. Some genotypes were associated to specific clinical forms and countries. MST1 genotype strains were associated to acute Q fever. A significant association was also found between clinical forms and plasmids. Strains harboring the QpRS plasmid were never found in acute Q fever and were only associated to persistent focalized infections. The QpDV and QpH1 plasmids were associated to acute Q fever. In addition, the Guyanese strain CB175, the most virulent strain to date, exhibited a unique MST genotype, a distinct COG profile and an important variation in gene number that may explain its unique pathogenesis. Therefore, strain-specific factors play an important role in determining the epidemiological and clinical manifestations of Q fever alongside with host-specific factors (valvular and vascular defects notably)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Abou Abdallah, Million, Delerce, Anani, Diop, Caputo, Zgheib, Rousset, Sidi Boumedine, Raoult and Fournier.)

Strain Marseille-P9829 was isolated from a bone sample collected from an open right fibula fracture from a 46-years old patient. Strain Marseille-P9829 (= CSUR P9829 = DSM 110695) was a Gram-negative, non-spore-forming and non-motile bacterium. This strain had a positive catalase activity but was oxidase-negative. The major fatty acids methyl esters were hexadecanoic acid (45.6%) and 9-hexadecenoic acid (28.4%). Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry analysis suggested that this strain belongs to the species Buttiauxella gaviniae. Since there were few reports of clinical infections with this species in humans, whole genome sequencing was performed and a polyphasic taxono-genomic approach was followed in order to verify the classification of strain Marseille-P9829. The 16S rRNA gene sequence BLAST against the NCBI database yielded the highest similarity of 99.8% with Buttiauxella agrestis, suggesting that strain Marseille-P9829 belongs to this species. However, genomic comparison by digital DNA-DNA hybridization showed that values between strain Marseille-P9829 and other validly published Buttiauxella species were all lower than 70%. Furthermore, all average nucleotide identities were lower than 95-96%. Therefore, these results confirmed that strain Marseille-P9829 belonged to a new Buttiauxella species for which we propose the name Buttiauxella massiliensis sp. nov., with strain Marseille-P9829 as type strain., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Strains Marseille-P2265 T (=CSUR P2265 T  =DSM 102082  T ) and Marseille-P3890 T (=CSUR P3890 T  =CCUG 72341  T ) were isolated from stool samples using the culturomics approach. The 16S rRNA gene sequences of both strains were sequenced and compared by BLASTn to the NCBI database. Strains Marseille-P2265 T and Marseille-P3890 T were most closely related to Acutalibacter muris with identities of 94.3% and 91.5%, respectively. Between the two strains, the 16S rRNA gene sequence identity was 91.5%. Both strains are anaerobic Gram-positive, oxidase- and catalase-negative. The major fatty acid methyl esters (> 10%) in both strains are C 16:0 and anteiso-C 15:0 . Additionally, strain Marseille-P2265 T has iso-C 15:0 and C 14:0 , and strain Marseille-P3890 T , iso-C 14:0 . Strain Marseille-P2265 T has a genome size of 3,671,396-bp with a G + C content of 52.8%. As for strain Marseille-P3890 T , the genome is 2,702,024-bp-long with a 39.8% G + C content. The genomic comparison of closely related species with strains Marseille-P2265 T and Marseille-P3890 T showed that all digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI) and average amino acid identity (AAI) values were lower than the published species thresholds (70% for dDDH, 95-96% for OrthoANI/AAI). Based on these results, it was concluded that strains Marseille-P2265 T and Marseille-P3890 T belong to two new genera in the family Oscillospiraceae. For these two genera, the names Neglectibacter gen. nov. and Scatolibacter gen. nov. were proposed, with strains Marseille-P2265 T and Marseille-P3890 T being the type strains of Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., respectively., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Bartonella species are reemerging infectious agents that are transmitted by arthropod vectors among animals and/or humans. At least 13 of the 35 currently recognized Bartonella species are pathogenic for humans. Most of the pathogenic species, except Bartonella quintana and Bartonella bacilliformis, are zoonotic agents with animal reservoirs, including cats, dogs, coyotes, foxes, cattle, and rodents. In this study, a novel Bartonella species was isolated from the blood of a Crocidura suaveolens (Pallas, 1811) Lesser shrew that was captured in the Bartın region of Northwestern Turkey. The strain, RSKK 19006, was characterized using whole-genome sequencing and comparison, multilocus sequence typing ( gltA, rpoB, ssrA, nuoG, and 16S rRNA) and internal transcribed spacer sequencing, electron microscopy scanning, biochemical tests, and MALDI-TOF MS (matrix assisted laser desorption ionization-time of flight mass spectrometry). This novel Bartonella is a Gram-negative, rod-shaped, microaerophilic bacterium and has neither flagella nor pilus. As a consequence, we propose to name this new species Bartonella refiksaydamii sp. nov. in Bartonella genus. The zoonotic potential of this novel Bartonella species is as yet unknown.

Five novel bacterial strains, Marseille-P1476 T (=CSURP1476 T =DSM 100642 T ), Marseille-P3256 T (=CSURP3256 T =CECT 9977 T ), Marseille-P2936 T (=CSURP2936 T =DSM 103159 T ), Marseille-P2912 T (=CSURP2912 T =DSM 103345 T ) and Marseille-P3197 T (=CSURP3197 T =CCUG 71847 T ), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella . A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476 T , Marseille-P2936 T and Marseille-P3197 T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912 T and Marseille-P3256 T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.

Lachnoclostridium phocaeense is a new species in the genus Lachnoclostridium . Lachnoclostridium phocaeense is a Gram-positive anaerobic rod. This strain, Marseille-P3177 T (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)., (© 2021 The Authors.)

An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551 T 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-P5551 T 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., (© 2021 The Authors.)

Here, we report the draft genome sequence of Vogesella oryzae L3B39 T (CSUR Q2602 T  = DSM 28780), which is a Vogesella species isolated from the rhizosphere of saline-tolerant pokkali rice. The genome sequence was assembled into 58 contigs for a total size of 3,415,129 bp, with a G+C content of 62.3%., (Copyright © 2021 Kangale et al.)

The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract.We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics.We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured.Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.

Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The origin of a cholera outbreak may be unclear, as recently in Algeria. In two patients from North Africa, Vibrio cholerae was isolated in the context of hepatobiliary tract infections without any known outbreak. Gallbladder and asymptomatic long-term carriers might play a role in the emergence of cholera.

In 2007, Salirhabdus euzebyi was first described as a bacterial isolate from a sea salt evaporation pond. As no genome sequence was previously available for this species, we performed whole-genome sequencing. The chromosome of strain Q1438 was 3,784,443 bp long with 36% G+C content, 3,830 protein-coding genes, and 74 RNA genes., (Copyright © 2020 Zgheib et al.)

Bartonella saheliensis strain 077 (= CSUR B644T; = DSM 28003T) is a new bacterial species isolated from blood of the rodent Gerbilliscus gambianus captured in the Sine-Saloum region of Senegal. In this work we describe the characteristics of this microorganism, as well as the complete sequence of the genome and its annotation. Its genome has 2 327 299 bp (G+C content 38.4%) and codes for 2015 proteins and 53 RNA genes., (© 2020 The Authors.)

We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01 T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15 T of 97.42 %. Their predominant fatty acid is iso-C 15 : 0 (73.8 % for strain BD 01 T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01 T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01 T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01 T was chosen as type strain of C. vietnamensis sp. nov.

Anaerosphaera massiliensis strain Marseille-P4592 T (= CSURP4592 T ; = CCUG72452 T ) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo., (© 2019 The Authors.)

A polyphasic taxono-genomic strategy was used to describe a new bacterium, strain Marseille-P1935; isolated from the gut of a healthy infant. 16S rRNA sequencing showed that the isolate belongs to the genus Haloimpatiens in the family Clostridiaceae . Phenotypic analysis and whole-genome sequence analyses confirm the status of the new species. We propose the creation of the new species Haloimpatiens massiliensis strain Marseille-P1935 T (= CSURP1935 T ; = DSM100591 T )., Competing Interests: None to declare., (© 2019 The Author(s).)

Strain 6021061333 T 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 KJ1R5 T , 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 6021061333 T 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 6021061333 T 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 6021061333 T (= CSUR P2660, = CECT 9670).

The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911 T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.

In 2016, Peptoniphilus catoniae was reported as a bacterial species isolated from a healthy Peruvian male. In 2018, a clinical strain from the same species was isolated from the stool of a French patient with kidney cancer. The genome of this strain, P8546, was 1,725,465 bp long, with 33.4% G+C content., (Copyright © 2019 Anani et al.)

Urinicoccus massiliensis strain Marseille-P1992 T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine., Competing Interests: The authors declare no conflicts of interest. This work was funded by the IHU Méditerranée Infection (Marseille, France) and by the French Government under the Investissements d’Avenir (Investments for the Future) programme managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research) (reference: Méditerranée Infection 10-IAHU- 03)., (© 2019 The Authors.)

In 2016, Haloimpatiens lingqiaonensis was described as a bacterial isolate from paper mill wastewater. Previously, no whole-genome sequence was available for this microorganism. Whole-genome sequencing of strain P8956 yielded a 3,295,388-bp genome with a 30.7% G+C content, 2,917 protein-coding genes, and 95 predicted RNA genes., (Copyright © 2019 Anani et al.)

Prevotella ihumii strain Marseille-P3385 T (= CSURP3385 T ; = DSM106428 T ) is a new species isolated from a fresh stool specimen of a healthy woman., (© 2019 The Author(s).)

Dorea phocaeensis strain Marseille-P4003 T (= CSURP4003 T ; = CCUG71359 T ) is a new species isolated from the stool of a healthy 29-year-old male from France., (© 2019 The Author(s).)

Enterococcus mediterraneensis strain Marseille-P4358 T (= CSURP4358 T ) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo., (© 2019 The Author(s).)

Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417 T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997 T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431 T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens., (© 2019 The Authors. Published by Elsevier Ltd.)

Strain Marseille-P4121 T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121 T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480 T , a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C 18:1ω9 (34.4%), C 16:0 (30.1%), and C 18:0 (19%). The draft genome size of strain Marseille-P4121 T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121 T (= CECT 9671 T  = CSUR P4121 T ) is the type strain of the new species Janibacter massiliensis sp. nov.

In 2013, Olivibacter jilunii was reported as a bacterial species isolated from contaminated soil. In 2018, a clinical strain from the same species was isolated from the rectal swab of a Hajj pilgrim. Genome sequencing yielded 6,704,032 bp, with 41.2% G+C content, 5,406 protein-coding genes, and 54 predicted RNA genes in strain P8502., (Copyright © 2019 Anani et al.)

Enterobacter timonensis strain mt20 T (= CSUR P2201 T , = DSM101775 T ) is a new species isolated from a fresh human stool specimen., (© 2019 The Author(s).)