Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota

Two new bacterial strains, Marseille-P2698^T (CSUR P2698 = DSM 103,121) and Marseille-P2260^T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698^T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260^T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698^T were C_{15:0 iso} (63%), C_{15:0 anteiso} (11%), and C_{17:0 3-OH iso} (8%). Those found in Marseille-P2260^T strain were C_16:00 (39%), C_18:1n9 (16%) and C_18:1n7 (14%). Strains Marseille-P2698^T and Marseille-P2260^T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneus^T, and of 90.98% and 95.07% with Odoribacter splanchnicus^T and Eubacterium sulci^T, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicus^T and E. sulci^T respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698^T and Marseille-P2260^T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.

Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis

The novel bacterial strain Marseille-P4005^T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058^T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005^T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005^T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005^T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005^T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.

Whole-genome sequencing and phylogenomic analyses of a novel zearalenone-degrading Bacillus subtilis B72

Bacillus strain B72 was previously isolated as a novel zearalenone (ZEN) degradation strain from the oil field soil in Xinjiang, China. The genome of B72 was sequenced with a 400 bp paired-end using the Illumina HiSeq X Ten platform. De novo genome assembly was performed using SOAPdenovo2 assemblers. Phylogenetic analysis using 16S rRNA gene sequencing demonstrated that B72 is closely related to the novel Bacillus subtilis (B. subtilis) strain DSM 10. A phylogenetic tree based on 31 housekeeping genes, constructed with 19 strains closest at the species level, showed that B72 was closely related to B. subtilis 168, B. licheniformis PT-9, and B. tequilensis KCTC 13622. Detailed phylogenomic analysis using average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) demonstrated that B72 might be classified as a novel B. subtilis strain. Our study demonstrated that B72 could degrade 100% of ZEN in minimal medium after 8 h of incubation, which makes it the fastest degrading strain to date. Moreover, we confirmed that ZEN degradation by B72 might involve degrading enzymes produced during the initial period of bacterial growth. Subsequently, functional genome annotation revealed that the laccase-encoding genes yfiH (gene 1743) and cotA (gene 2671) might be related to ZEN degradation in B72. The genome sequence of B. subtilis B72 reported here will provide a reference for genomic research on ZEN degradation in the field of food and feed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03517-y.

Characterization and Whole-Genome Analysis of a Zearalenone-Degrading Stappia sp. WLB 29

Zearalenone (ZEN) is a widely distributed mycotoxin that frequently contaminates crops and animal feed. Our previous studies showed that a new strain, Stappia sp. WLB 29 with a 97.47% of similarity to Stappia indica B106^T, isolated from the soil samples in the rhizosphere of the crops in Xinjiang, was capable of effectively degrading ZEN in minimal medium. In this study, we determined the complete genomic sequence of the Stappia sp. WLB 29 (Genbank accession number: JALBGD000000000; BioProject ID in GenBank is PRJNA814005). The total length of all sequences was 4,745,415 bp with a GC content of 67.08%. Moreover, the genome-wide analysis showed the presence of laccase- and peroxiredoxin-encoding genes in Stappia sp. WLB 29, which may be associated with ZEN degradation. The genome sequence of Stappia sp. WLB 29 reported here will serve as a reference for comparative genomic studies of ZEN degradation in the feed and food industry.

Understanding the Role of the Microbiome in Cancer Diagnostics and Therapeutics by Creating and Utilizing ML Models

Recent studies have highlighted that gut microbiota can alter colorectal cancer susceptibility and progression due to its impact on colorectal carcinogenesis. This work represents a comprehensive technical approach in modeling and interpreting the drug-resistance mechanisms from clinical data for patients diagnosed with colorectal cancer. To accomplish our aim, we developed a methodology based on evaluating high-performance machine learning models where a Python-based random forest classifier provides the best performance metrics, with an overall accuracy of 91.7%. Our approach identified and interpreted the most significant genera in the cases of resistant groups. Thus far, many studies point out the importance of present genera in the microbiome and intend to treat it separately. The symbiotic bacterial analysis generated different sets of joint feature combinations, providing a combined overview of the model’s predictiveness and uncovering additional data correlations where different genera joint impacts support the therapy-resistant effect. This study points out the different perspectives of treatment since our aggregate analysis gives precise results for the genera that are often found together in a resistant group of patients, meaning that resistance is not due to the presence of one pathogenic genus in the patient microbiome, but rather several bacterial genera that live in symbiosis.

Buttiauxella massiliensis sp. nov., Isolated from a Human Bone Infection

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.

Draft Genome Sequence of an NDM-1-Producing Sequence Type 101 (ST101) Klebsiella pneumoniae Strain, Marseille-Q1949

A pan-drug-resistant Klebsiella pneumoniae strain was isolated from the blood of a 70-year-old critically ill patient in April 2019. Interestingly, the patient recovered and was discharged home a month later. The genome of strain Marseille-Q1949 is 5,607,584 bp long and has a 57.1% G+C content and 5,467 protein-coding genes.

New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella

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.

Chitinophaga vietnamensis sp. nov., a multi-drug resistant bacterium infecting humans

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.