Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov

Correction: Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study

[This corrects the article DOI: 10.1371/journal.pone.0230895.].

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken

Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870T=LMG 32876T), Limosilactobacillus galli sp. nov. (DSM 113833T=LMG 32623T), Limosilactobacillus avium sp. nov. (DSM 113849T=LMG 32671T), Limosilactobacillus pulli sp. nov. (DSM 115077T=LMG 32877T), Limosilactobacillus viscerum sp. nov. (DSM 113835T=LMG 32625T), Limosilactobacillus difficilis sp. nov. (DSM 114195T=LMG 32875T) and Clostridium butanoliproducens (DSM 115076T=LMG 32878T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Faecalispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860T=LMG 32675T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species Clostridium jeddahense and Clostridium sporosphaeroides to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.

Caproicibacterium lactatifermentans sp. nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor

Two recently reported bacterial strains that were identified as the dominant caproate-producing bacteria in pit clay, were further characterized to determine their phylogeny and taxonomy. The two strains, designated as LBM19010^T and JNU-WLY1368, were short rod-shaped, Gram-stain-positive, non-motile and strictly anaerobic. Analysis of the 16S rRNA gene sequences revealed that strains LBM19010^T and JNU-WLY1368 shared a 16S rRNA gene sequence similarity of 99.93 % and belonged to a recent proposed genus Caproicibacterium in the family Oscillospiraceae. The proposed type strain, LBM19010^T, showed the highest 16S rRNA gene sequence similarity to Caproicibacterium amylolyticum LBM18003^T (96.34%), followed by Caproiciproducens galactitolivorans JCM 30532^T (94.14 %). The pairwise average nucleotide identity and average amino acid identity values between strains LBM19010^T and LBM18003^T were 74.84 and 76.18 %, respectively. Growth of strain LBM19010^T occurred at pH 4.5-7.5 (optimum, pH 5.0-5.5), 20-40 °C (optimum, 35 °C) and with 0-1 % (w/v) NaCl (optimum, 0 %). Strains LBM19010^T and JNU-WLY1368 were both able to ferment several hexoses, disaccharides, starch and lactate but not pentoses. Caproate and butyrate were the major end-products from glucose. The predominant cellular fatty acids (>10 %) of strain LBM19010^T were C_16 : 0 (56.3 %), C_14 : 0 DMA (19.5 %) and C_14 : 0 (14.9 %). The identified polar lipids of strain LBM19010^T were diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and nine unidentified glycolipids. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strains LBM19010^T and JNU-WLY1368 belong to a novel species of the genus Caproicibacterium, for which the name Caproicibacterium lactatifermentans sp. nov. is proposed. The type strain is LBM19010^T (=GDMCC 1.1627^T=JCM 33782^T).

Caproicibacterium amylolyticum gen. nov., sp. nov., a novel member of the family Oscillospiraceae isolated from pit clay used for making Chinese strong aroma-type liquor

An anaerobic, Gram-stain-positive, rod-shaped, motile and spore-forming bacterium, designated strain LBM18003^T, was isolated from pit clay used for making Chinese strong aroma-type liquor. Growth occurred at 20-40 °C (optimum, 30-37 °C), pH 4.5-9.5 (optimum, pH 6.5-7.0) and in the presence of 0.0-1.0 % (w/v) sodium chloride (optimum, 0 %). The predominant fatty acids were C_16:0, C_14:0, C_14:0 DMA and C_16:0 3-OH, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids and nine unidentified glycolipids. Phylogenetic analysis revealed that strain LBM18003^T is a novel member of the family Oscillospiraceae. The 16S rRNA gene sequence similarities of strain LBM18003^T to its two most closely related species were less than 94.5 % for distinguishing genera, i.e. closely related to Caproiciproducens galactitolivorans JCM 30532^T (94.1 %) and Caproicibacter fermentans DSM 107079^T (93.2 %). The genome size of strain LBM18003^T was 2 996 201 bp and its DNA G+C content was 48.48 mol%. Strain LBM18003^T exhibited 67.8 and 68.1% pairwise-determined whole-genome average nucleotide identity values to Caproiciproducens galactitolivorans JCM 30532^T and Caproicibacter fermentans DSM 107079^T, respectively; and showed 62.2 and 61.0 % the average amino acid identity values to Caproiciproducens galactitolivorans JCM 30532^T and Caproicibacter fermentans DSM 107079^T, respectively; and demonstrated 46.1 and 41.5 % conserved genes to Caproiciproducens galactitolivorans JCM 30532^T and Caproicibacter fermentans DSM 107079^T, respectively. The comparisons of 16S rRNA gene and genome sequences confirmed that strain LBM18003^T represented a novel genus of the family Oscillospiraceae. Based on morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, strain LBM18003^T represents a novel species of a novel genus of the family Oscillospiraceae, for which the name Caproicibacterium amylolyticum gen. nov., sp. nov. is proposed. The type strain is LBM18003^T (=GDMCC 1.1626^T=JCM 33783^T).

Draft genome sequence of Clostridium jeddahense EE-R19 isolated from an anaerobic digester

OBJECTIVES

Clostridium species of the order Clostridiales are mostly strictly anaerobic rod-shaped bacteria. They can be detected in a variety of environments, including the intestines of humans and animals, soil, water, and biogas reactors. Species of the genus Clostridium are widely used in various biotechnological processes, but several of them have been identified as significant human pathogens. Therefore, investigation at the genome level is necessary to provide valuable information about the ecology, genetics, and phylogenetic diversity of various Clostridium species.

DATA DESCRIPTION

In the present study, we report the whole genome sequence of Clostridium jeddahense strain EE-R19, which was isolated from a mesophilic anaerobic digester. The draft genome of C. jeddahense EE-R19 consisted of 59 contigs (> 500 bp), which amounted to 3,562,974 with an overall G + C content of 51.79%. The whole genome shotgun project of C. jeddahense EE-R19 has been deposited at DDBJ/ENA/GenBank under the accession number JAAVNF000000000.

Hydrogeniiclostidium mannosilyticum gen. nov., sp. nov. isolated from human faeces

A strain of obligately anaerobic, spore-forming, Gram-positive rods was isolated from child faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole genome sequencing revealed the strain to represent a member of the family Ruminococcaceae distant from described species and genera. The strain was moderately saccharolytic with mannose as the preferred substrate and produced lactic acid, acetic acid and H₂ as the end products. The major cellular long-chain fatty acids were C_16 : 0 and C_16 : 0 aldehyde. The genomic DNA G+C content was 52.3 mol%. On the basis of chemotaxonomic and genomic properties it was concluded that the strain represents a novel species in a new genus within the family Ruminococcaceae, for which the name Hydrogeniiclostidium mannosilyticum gen. nov., sp. nov. is proposed. The type strain of Hydrogeniiclostidium mannosilyticum is ASD2818^T (=VKM B-3268^T=JCM 33295^T).

From Culturomics to Clinical Microbiology and Forward

Culturomics has permitted discovery of hundreds of new bacterial species isolated from the human microbiome. Profiles generated by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry have been added to the mass spectrometer database used in clinical microbiology laboratories. We retrospectively collected raw data from MALDI-TOF mass spectrometry used routinely in our laboratory in Marseille, France, during January 2012-March 2018 and analyzed 16S rDNA sequencing results from misidentified strains. During the study period, 744 species were identified from clinical specimens, of which 21 were species first isolated from culturomics. This collection involved 105 clinical specimens, accounting for 98 patients. In 64 cases, isolation of the bacteria was considered clinically relevant. MALDI-TOF mass spectrometry was able to identify the species in 95.2% of the 105 specimens. While contributing to the extension of the bacterial repertoire associated with humans, culturomics studies also enlarge the spectrum of prokaryotes involved in infectious diseases.

Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces

Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.

Molecular characterization, antimicrobial resistance and clinico-bioinformatics approaches to address the problem of extended-spectrum β-lactamase-producing Escherichia coli in western Saudi Arabia

The goal of this study was to genotypically characterize extended-spectrum β-lactamase-producing Escherichia coli isolates from the western region of Saudi Arabia and to identify active antibiotics against these isolates using phenotypic and molecular modeling. In total, 211 ESBL-producing E. coli isolates recovered from heterogeneous clinical specimens were identified by MALDI-TOF. Thirty-two sequence types (STs) were identified from a multilocus sequence typing (MLST) analysis of ESBL-producing E. coli, including a novel ST (ST8162). The most common ST in the Saudi and expatriate population was ST131, followed by ST38. All the isolates were multidrug resistant (MDR), and >95% of the isolates were resistant to third-generation (ceftriaxone and ceftazidime) and fourth-generation (cefepime) cephalosporins. The ESBL-positive E. coli isolates primarily harbored the bla_CTX-M and bla_TEM genes. No resistance was observed against the carbapenem antibiotic group. All the ESBL-producing E. coli isolates were observed to be susceptible to a ceftazidime/avibactam combination. Molecular interaction analyses of the docked complexes revealed the amino acid residues crucial for the binding of antibiotics and inhibitors to the modeled CTX-M-15 enzyme. Importantly, avibactam displayed the most robust interaction with CTX-M-15 among the tested inhibitors in the docked state (∆G = −6.6 kcal/mol). The binding free energy values for clavulanate, tazobactam and sulbactam were determined to be −5.7, −5.9 and −5.2 kcal/mol, respectively. Overall, the study concludes that ‘ceftazidime along with avibactam’ should be carefully used as a treatment option against only carbapenem-resistant MDR ESBL-producing E. coli in this region.

Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics

The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2T , the second Intestinimonas species cultured from the human gut

Intestinimonas massiliensis sp. nov strain GD2^T is a new species of the genus Intestinimonas (the second, following Intestinimonas butyriciproducens gen. nov., sp. nov). First isolated from the gut microbiota of a healthy subject of French origin using a culturomics approach combined with taxono-genomics, it is strictly anaerobic, nonspore-forming, rod-shaped, with catalase- and oxidase-negative reactions. Its growth was observed after preincubation in an anaerobic blood culture enriched with sheep blood (5%) and rumen fluid (5%), incubated at 37°C. Its phenotypic and genotypic descriptions are presented in this paper with a full annotation of its genome sequence. This genome consists of 3,104,261 bp in length and contains 3,074 predicted genes, including 3,012 protein-coding genes and 62 RNA-coding genes. Strain GD2^T significantly produces butyrate and is frequently found among available 16S rRNA gene amplicon datasets, which leads consideration of Intestinimonas massiliensis as an important human gut commensal.

Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man

A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518^T, was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518^T can grow in a medium with 0-20% (w/v) sodium chloride (optimally at 5-7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518^T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518^T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518^T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518^T (CSUR P3518T, DSM69894).

Genome sequence and description of Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of patient with kwashiorkor

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.

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.

Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.

Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France

Strain GD1(T) gen. nov., sp. nov., is the type strain of the newly proposed genus and species Drancourtella massiliensis, belonging to the Clostridiales order. This strain, isolated from the stool of a healthy person, is a Gram-positive rod, oxygen intolerant and nonmotile, with spore-forming activity. The features of this organism and its genome sequence are described. The draft genome is 3 057 334 bp long with 45.24% G + C content; it contains 2861 protein-coding genes and 64 RNA genes.

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.