Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut

Bacillus litorisediminis sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment

Two aerobic, Gram-staining-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-47801^T and FJAT-47835, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. Growth was observed at 25-55 °C (optimum, 50 °C) and pH 7.0-9.0 (optimum, pH 7.0), with up to 4.0% (w/v) NaCl (optimum, without NaCl). Strains FJAT-47801^T and FJAT-47835 showed the highest 16S rRNA gene sequence similarity to Bacillus oleivorans (98.5%). The 16S rRNA gene sequence similarity between FJAT-47801^T and FJAT-47835 was 99.9% indicating they were the same species. Phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 120 conserved bacterial single-copy genes) trees showed that strains FJAT-47801^T and FJAT-47835 should be affiliated to the genus Bacillus. The of menaquinone of strain FJAT-47801^T was MK-7. The major fatty acids of strain FJAT-47801^T were iso-C_15:0, anteiso-C_15:0, iso-C_17:0, and C_16:0. The major polar lipids strain FJAT-47801^T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The genomic DNA G+C content of strain FJAT-47801^T was 39.3%. The average nucleotide identity (84.3%) and the digital DNA-DNA hybridization value (28.1%) between strain FJAT-47801^T and B. oleivorans CCTCC AB 2013353^T were below the cut-off level for species delineation. Based on the above results, strain FJAT-47801^T represents a novel species of the genus Bacillus, for which the name Bacillus litorisediminis sp. nov., is proposed. The type strain is FJAT-47801^T (=GDMCC 1.2712^T = JCM 34875^T).

Bacillus pasinlerensis sp. nov., a thermophilic bacterium isolated from a hot spring in Turkey

A Gram-reaction-positive, endospore-forming bacterium, designated strain P1^T, was isolated from water samples collected from Pasinler Hot Spring and characterized using a polyphasic approach to clarify its taxonomic position. Strain P1^T was found to have chemotaxonomic and morphological characteristics consistent with its classification in the genus Bacillus. The strain shared the highest 16S rRNA gene sequence identity values with Bacillus thermolactis R-6488^T (97.6 %) and Bacillus kokeshiiformis MO-04^T (97.2 %) and formed a distinct clade with both type strains in the phylogenetic trees based on 16S rRNA gene sequences. Strain P1^T could grow optimally at 55 °C and in the presence of 2 % NaCl. The organism was found to contain meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The predominant menaquinone was determined to be MK-7. The major cellular fatty acids were identified as iso-C_15 : 0, iso-C_17 : 0 and anteiso-C_17 : 0. Based upon the consensus of phenotypic and phylogenetic analyses, strain P1^T represents a novel species of the genus Bacillus, for which the name Bacillus pasinlerensis sp. nov. is proposed. The type strain is P1^T (=DSM 107529^T=CECT 9885^T=NCCB 100674^T).

Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu

A Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated as 3 H-10^T, was isolated from a yellow water sample collected from the manufacturing process of strong flavor Chinese baijiu in Yibin region of Sichuan province (PR China). Oval endospores were formed at the subtermini of cells with swollen sporangia. The isolate was able to grow at temperatures of 20-45 °C (optimum growth at 37 °C), at pH 6.0-10.0 (optimum growth at pH 8.0) and in the presence of 0-2 % (w/v) NaCl (optimum growth with 0 % NaCl). Ribose was the major cell-wall sugar, and meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of 3 H-10^T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). MK-7 was predominant menaquinone and iso-C_15 : 0 (60.7 %) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that 3 H-10^T was most closely related to Bacillus mesophilus SA4^T (96.30 %), Bacillus ginsengihumi Gsoil 114^T (96.27 %) and Bacillus shackletonii LMG 18435^T (96.27 %). The average nucleotide identity (ANI) values between strain 3 H-10^T and the three type strains mentioned above were 69.56, 70.19 and 70.67 %, respectively. The genomic DNA G+C content was 35.4 mol%. On the basis of its phenotypic, chemotaxonomic and phylogenetic properties, strain 3 H-10^T represents a novel species of the genus Bacillus, for which the name Bacillus aquiflavi sp. nov. is proposed. The type strain is Bacillus aquiflavi 3 H-10^T (=CICC 24755^T=JCM 33703^T).

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

Description of Bacillus kexueae sp. nov. and Bacillus manusensis sp. nov., isolated from hydrothermal sediments

Two Gram-staining-positive, strictly aerobic bacilli, designated as strains Ma50-5^T and Ma50-6^T, were isolated from the hydrothermal sediments of Manus Basin in the western Pacific Ocean. Based on 16S rRNA gene sequence, strains Ma50-5^T and Ma50-6^T were most closely related to Bacillus alveayuensis (97.0 and 97.2 % identity, respectively). The 16S rRNA gene sequence identity between strains Ma50-5^T and Ma50-6^T was 97.4 %. The identities between strains Ma50-5^T and Ma50-6^T and other closely related organisms were below 97.0 %. The G+C contents of the genomic DNA of strains Ma50-5^T and Ma50-6^T were 43.4 and 47.6 mol%, respectively. The major fatty acids (>10 %) of both strains were iso-C15 : 0 and iso-C17 : 0. The predominant isoprenoid quinone detected in both strains was menaquinone-7. Phylogenetic, physiological, biochemical and morphological analyses suggested that strains Ma50-5^T and Ma50-6^T represent two novel species of the genus Bacillus, for which the names Bacillus kexueae sp. nov. (type strain Ma50-5^T=KCTC 33881^T=CCTCC AB 2017020^T) and Bacillus manusensis sp. nov. (type strain Ma50-6^T=KCTC 33882^T=CCTCC AB 2017019^T), respectively, are proposed.

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host) to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation), a depletion in oxygen-sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.