Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout

The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.

Fermentation Blues: Analyzing the Microbiota of Traditional Indigo Vat Dyeing in Hunan, China

Traditional indigo dyeing through anaerobic fermentation has recently gained worldwide attention in efforts to address concerns regarding the sustainability of industrial indigo dyeing and the impact of toxic reducing agents such as sodium dithionite (Na2S2O4) on human health and the ecological environment. Intriguingly, changes in the microbiota during indigo fermentation are known to potently affect the onset of indigo reduction, and thus elucidation of the microbial community transitions could help develop methods to control the initiation of indigo reduction. Here, we investigated the microbiota associated with the traditional indigo dyeing practiced in Hunan, China. Specifically, we identified the bacterial and fungal components of the microbiota at distinct stages in the indigo fermentation process by analyzing 16S rRNA gene and internal transcribed spacer sequences. Our analyses revealed two substantial changes in the microbiota during the traditional indigo fermentation process. The first change, which was probably caused by the introduction of Chinese liquor (featuring a high alcohol concentration), resulted in decreased bacterial diversity and increased proportions of Pseudomonas, Stenotrophomonas, and Bacillaceae family members. The second change, which could be attributed to the addition of specific plant species, led to an increase in the abundance of Alkalibacterium, Amphibacillus, the obligate anaerobe Turicibacter, the facultative anaerobe Enterococcus, and ZOR0006, as well as to a decrease in the pH and redox potential values. Our results indicate that the specific plant mixture included in the procedure here could be used as an effective additive to accelerate the initiation of indigo reduction during the fermentation process. To the best of our knowledge, this is the first report revealing the fungal diversity during the indigo fermentation process and, furthermore, showing that the fungal diversity has remained in transition despite the relatively stable bacterial diversity in the proper indigo fermentation process. Although traditional indigo fermentation in China is challenging to manage, we can benefit from local knowledge of the fermentation process, and understanding the scientific bases of traditional indigo fermentation will facilitate the development of environmentally friendly procedures. IMPORTANCE Chemical reducing agents included in modern indigo dyeing to initiate indigo reduction can be harmful to both human health and the environment. Given that traditional indigo dyeing involves natural fermentation in a dye vat using natural organic additives without the use of toxic chemicals and that changes in the microbiota during traditional indigo fermentation potently affect the onset of indigo reduction, elucidation of these microbial community transitions could help develop methods to control the initiation of indigo reduction. This study on the microbiota associated with the traditional indigo dyeing practiced in Hunan, China, has identified the bacterial and fungal communities at distinct stages of the indigo fermentation process. Notably, the addition of specific plant species might yield the desired microbial communities and appropriate fermentation conditions, which could be used as an effective additive to accelerate the initiation of indigo reduction. This study has also revealed the fungal diversity during the indigo fermentation process for the first time and shown that the fungal diversity has remained in transition despite the relatively stable bacterial diversity. Thus, this work provides new insights into the traditional indigo fermentation process used in China and substantially enhances current efforts devoted to designing environmentally friendly methods for industrial indigo dyeing.

Oceanobacillus saliphilus sp. nov., Isolated from Saline-Alkali Soil in Heilongjiang Province, China

A novel bacterium, designated strain APA_H-1(4)^T, was isolated from the saline-alkaline soil, Zhaodong, Heilongjiang Province, China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus, and showed the highest sequence similarity to O. damuensis KCTC 33146^T (98.35%, similarity) and 'O. massiliensis' DSM 24644 (98.32%). The average nucleotide identity values between strain APA_H-1(4)^T and other members of the genus Oceanobacillus were lower than 82% recommended for distinguishing novel prokaryotic species. The digital DNA-DNA hybridization values of strain APA_H-1(4)^T with O. damuensis KCTC 33146^T and 'O. massiliensis' DSM 24644 were 13.60 and 17.60%, respectively. Cells of strain APA_H-1(4)^T were Gram-staining positive, motile, aerobic, spore-forming rods (0.5-0.7 × 1.8-2.6 μm) with flagella. The growth was found to occur optimally at 37 °C. The whole-cell hydrolysate contained meso-diaminopimelic acid as the diagnostic cell wall diamino acid. The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified polar lipid. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). The major cellular fatty acid (>10%) was anteiso-C_15:0. The G + C content of the genomic DNA was determined to be 38.4% based on the draft genome sequence. Based on the comparative analysis of polyphasic taxonomic data, strain APA_H-1(4)^T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus saliphilus sp. nov. is proposed. The type strain is APA_H-1(4)^T (=GDMCC 1.2239^T = KCTC 43254^T).

Oceanobacillus alkalisoli sp. nov., an alkaliphilic bacterium isolated from saline-alkaline soil

Two alkaliphilic strains, designated APA_J-2 (6-2)T and APA_J-5 (13-2), were isolated from saline-alkali soil sampled in Jilin Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains APA_J-2 (6-2)T and APA_J-5(13–2) were closely related to members of the genus Oceanobacillus , and had the highest sequence similarity to Oceanobacillus indicireducens JCM 17251T (96.8 and 96.9 %, respectively). The 16S rRNA gene sequence similarity between the two novel isolates was 99.6 %, indicating that they were similar species. Cells were Gram-stain-positive, aerobic, motile and rod-shaped. The strains grew at 15–45 °C (optimum, 37 °C), pH 8.0–11.0. (optimum, pH 9) and with 0–10 % (w/v) NaCl (optimum, 5 %). The strains contained menaquinone-7 as the respiratory quinone and anteiso-C15 : 0 as the predominant cellular fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 40.0 mol%. The average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values of strain APA_J-2 (6-2)T with O. indicireducens JCM 17251T were 85.5, 87.9 and 30.7 %, respectively. The ANI, AAI and dDDH values of strain APA_J-5 (13-2) with O. indicireducens JCM 17251T were 85.7, 87.7 and 30.8 %, respectively. Based on the phylogenetic, phenotypic, biochemical, chemotaxonomic and genome data, strains APA_J-2 (6-2)T and APA_J-5 (13-2) represent a novel species of the genus Oceanobacillus , for which the name Oceanobacillus alkalisoli sp. nov. is proposed. The type strain is APA_J-2 (6-2)T (=KCTC 43253T=GDMCC 1.2242T).

Fundicoccus fermenti sp. nov., an indigo-reducing facultative anaerobic alkaliphile isolated from indigo fermentation liquor used for dyeing

Two facultative anaerobic and facultative alkaliphilic indigo-reducing strains, designated F-1^T and F-2, were isolated from indigo fermentation liquor produced from couched woad fermentation-based Indian indigo fermentation fluid. The 16S rRNA gene phylogeny showed that Fundicoccus ignavus WS4937^T (99.5%) was the closest neighbour of F-1^T. The isolated bacterial cells were Gram-stain-positive and facultative anaerobic coccoids. Strain F-1^T grew at between 5 and 37 °C with optimum growth between 28‒32 °C. The isolate grew in a pH range of 7.0‒10.5, with optimum growth between pH 9.0‒10.5. The DNA G+C content was 37.6 mol% (HPLC). The whole-cell fatty acid profile mainly consisted (>10 %) of C_16 : 0, C_16 : 1 ω9c, C_18 : 0 and C_18 : 1 ω9c. The digital DNA-DNA hybridization value between strain F-1^T and F. ignavus WS4937^T was 52.9 %. Based on their physiological and biochemical characteristics, and phylogenetic and genomic data, the isolates can be discriminated from F. ignavus WS4937^T. The name Fundicoccus fermenti sp. nov. is proposed. The type strain of this species is F-1^T (JCM 34140^T=NCIMB 15255^T).

Isolation and characterization of indigo-reducing bacteria and analysis of microbiota from indigo fermentation suspensions

In natural indigo dyeing, the water-insoluble indigo included in the composted indigo leaves called sukumo is converted to water-soluble leuco-indigo through the reduction activities of microorganisms under alkaline conditions. To understand the relationship between indigo reduction and microorganisms in indigo-fermentation suspensions, we isolated and identified the microorganisms that reduce indigo and analyzed the microbiota in indigo-fermentation suspensions. Indigo-reducing microorganisms, which were not isolated by means of a conventional indigo carmine-reduction assay method, were isolated by using indigo as a direct substrate and further identified and characterized. We succeeded in isolating bacteria closely related to Corynebacterium glutamicum, Chryseomicrobium aureum, Enterococcus sp. for the first time. Anthraquinone was found to be an effective mediator that facilitated the indigo-reduction activity of the isolated strains. On analysis of the microbiota in indigo-fermentation suspensions, the ratio of indigo-reducing bacteria and others was found to be important for maintaining the indigo-reduction activity.

Characterization of the microbiota in long- and short-term natural indigo fermentation

The duration for which the indigo-reducing state maintenance in indigo natural fermentation in batch dependent. The microbiota was analyzed in two batches of sukumo fermentation fluids that lasted for different durations (Batch 1: less than 2 months; Batch 2: nearly 1 year) to understand the mechanisms underlying the sustainability and deterioration of this natural fermentation process. The transformation of the microbiota suggested that the deterioration of the fermentation fluid is associated with the relative abundance of Alcaligenaceae. Principal coordinates analysis (PCoA) showed that the microbial community maintained a very stable state in only the long-term Batch 2. Therefore, entry of the microbiota into a stable state under alkaline anaerobic condition is an important factor for maintenance of indigo fermentation for long duration. This is the first report on the total transformation of the microbiota for investigation of long-term maintenance mechanisms and to address the problem of deterioration in indigo fermentation.

Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments

Indigo fermentation, which depends on the indigo-reducing action of microorganisms, has traditionally been performed to dye textiles blue in Asia as well as in Europe. This fermentation process is carried out by naturally occurring microbial communities and occurs under alkaline, anaerobic conditions. Therefore, there is uncertainty regarding the fermentation process, and many unknown microorganisms thrive in this unique fermentation environment. Until recently, there was limited information available on bacteria associated with this fermentation process. Indigo reduction normally occurs from 4 days to 2 weeks after initiation of fermentation. However, the changes in the microbiota that occur during the transition to an indigo-reducing state have not been elucidated. Here, the structural changes in the bacterial community were estimated by PCR-based methods. On the second day of fermentation, a large change in the redox potential occurred. On the fourth day, distinct substitution of the genus Halomonas with the aerotolerant genus Amphibacillus was observed, corresponding to marked changes in indigo reduction. Under open-air conditions, indigo reduction during the fermentation process continued for 6 months on average. The microbiota, including indigo-reducing bacteria, was continuously replaced with other microbial communities that consisted of other types of indigo-reducing bacteria. A stable state consisting mainly of the genus Anaerobacillus was also observed in a long-term fermentation sample. The stability of the microbiota, proportion of indigo-reducing microorganisms, and appropriate diversity and microbiota within the fluid may play key factors in the maintenance of a reducing state during long-term indigo fermentation. Although more than 10 species of indigo-reducing bacteria were identified, the reduction mechanism of indigo particle is riddle. It can be predicted that the mechanism involves electrons, as byproducts of metabolism, being discarded by analogs mechanisms reported in bacterial extracellular solid Fe3+ reduction under alkaline anaerobic condition.

Azoreductase from alkaliphilic Bacillus sp. AO1 catalyzes indigo reduction

Indigo is an insoluble blue dye historically used for dyeing textiles. A traditional approach for indigo dyeing involves microbial reduction of polygonum indigo to solubilize it under alkaline conditions; however, the mechanism by which microorganisms reduce indigo remains poorly understood. Here, we aimed to identify an enzyme that catalyzes indigo reduction; for this purpose, from alkaline liquor that performed microbial reduction of polygonum indigo, we isolated indigo carmine-reducing microorganisms. All isolates were facultative anaerobic and alkali-tolerant Bacillus spp. An isolate termed AO1 was found to be an alkaliphile that preferentially grows at pH 9.0-11.0 and at 30-35 °C. We focused on flavin-dependent azoreductase as a possible enzyme for indigo carmine reduction and identified its gene (azoA) in Bacillus sp. AO1 using homology-based strategies. azoA was monocistronic but clustered with ABC transporter genes. Primary sequence identities were < 50% between the azoA product (AzoA) and previously characterized flavin-dependent azoreductases. AzoA was heterologously produced as a flavoprotein tolerant to alkaline and organic solvents. The enzyme efficiently reduced indigo carmine in an NADH-dependent manner and showed strict specificity for electron acceptors. Notably, AzoA oxidized NADH in the presence, but not the absence, of indigo. The reaction rate was enhanced by adding organic solvents to solubilize indigo. Absorption spectrum analysis showed that indigo absorption decreased during the reaction. These observations suggest that AzoA can reduce indigo in vitro and potentially in Bacillus sp. AO1. This is the first study that identified an indigo reductase, providing a new insight into a traditional approach for indigo dyeing.

Insight into the bacterial diversity of fermentation woad dye vats as revealed by PCR-DGGE and pyrosequencing

The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.

Development of media to accelerate the isolation of indigo-reducing bacteria, which are difficult to isolate using conventional media

Indigo-reducing bacteria perform natural fermentation in indigo fermentation fluid. Owing to the stochastic nature of the process, the constituent in indigo fermentation fluid differ depending on the prepared batch and fermentation period. To identify new indigo-reducing bacteria, isolation of the bacteria is indispensable. However, isolation of indigo-reducing bacteria is difficult because conventional media are often unsuitable to isolate these slow-growing bacteria that also exist in low numbers. Hydrolysates of polysaccharides and mixtures of plant base constituents are candidates to accelerate the isolation of indigo-reducing bacteria that cannot be isolated using conventional media. In this current study, wheat bran hydrolysate and composted indigo leaves (sukumo) were used as ingredients in the fermentation fluid in the selective medium for indigo-reducing bacteria in anaerobic culture. The results suggested that obligate and oxygen-non-metabolizing facultative anaerobes are difficult to isolate using conventional media, whereas oxygen-metabolizing facultative anaerobes, relatively rapid-growing and major bacterial strains are relatively easy to isolate. Media containing sukumo hydrolysate facilitated the isolation of novel species of Bacillus pseudofirmus-related strains, whereas media containing wheat bran hydrolysate facilitated the isolation of Amphibacillus spp. (including new species). Seven species (including two new species) of indigo-reducing bacteria were isolated using wheat bran hydrolysate-containing media, whereas six species (including three new species) of indigo-reducing bacteria were isolated using media containing both wheat bran and sukumo hydrolysates. These newly developed culture media will facilitate the isolation of unknown bacteria in indigo fermentation and in environments similar to indigo fermentation fluid.

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov

Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.

Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

Strain Vm-5(T) was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5(T) (CSUR P971 = DSM 28587).

Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut

Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100 g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175 bp long genome exhibits a G + C content of 39.15 % and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.

Oceanobacillus arenosus sp. nov., a moderately halophilic bacterium isolated from marine sand

A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterium, designated CAU 1183T, was isolated from marine sand and its taxonomic position was investigated by using a polyphasic approach. The bacterium grew optimally at 30 °C, at pH 8.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1183T formed a distinct lineage within the genus Oceanobacillus and exhibited the highest similarity to Oceanobacillus chungangensis CAU 1051T (97.6 %). The strain contained MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0 was the major cellular fatty acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polar lipid pattern of strain CAU 1183T consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified lipids, including two phospholipids, two glycolipids, a phosphoglycolipid and two lipids. The G+C content of the genomic DNA was 37.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CAU 1183T should be assigned to a novel species in the genus Oceanobacillus, for which the name Oceanobacillus arenosus sp. nov. is proposed. The type strain is CAU 1183T ( = KCTC 33037T = CECT 8560T).

Oceanobacillus bengalensis sp. nov., a bacterium isolated from seawater of the Bay of Bengal

A Gram-stain positive, motile, and subterminal endospore-forming rod-shaped bacterium, designated strain Ma-21(T), was isolated from seawater of the Bay of Bengal. Strain Ma-21(T) was found to grow optimally at 37 °C and pH 8.0 with 3% (w/v) NaCl. Phylogenetic analyses showed that strain Ma-21(T) forms a distinct phylogenetic lineage close to Oceanobacillus chungangensis CAU 1051(T), Oceanobacillus caeni S-11(T), Oceanobacillus arenosus CAU 1183(T), Oceanobacillus halophilum GD01(T) and Ornithinibacillus heyuanensis GIESS003(T) in the family Bacillaceae. The cell wall of strain Ma-21(T) was found to contain meso-diaminopimelic acid as the diagnostic diamino acid, which is in line with those of members of the genus Oceanobacillus. The genomic DNA G+C content was determined to be 35.9 mol%. The only respiratory quinone detected was MK-7. The major cellular fatty acids were identified as anteiso-C(15:0) and anteiso-C(17:0). The major polar lipids were found to be diphosphatidylglycerol and phosphatidylglycerol. On the basis of phylogenetic, chemotaxonomic and phenotypic properties, strain Ma-21(T) is suggested to represent a novel species in the genus Oceanobacillus, for which the name Oceanobacillus bengalensis sp. nov. is proposed. The type strain is Ma-21(T) (=CGMCC 1.12799(T) = KCTC 33416(T) = MCCC 1K00260(T)).

Sinibacillus soli gen. nov., sp. nov., a moderately thermotolerant member of the family Bacillaceae

Two Gram-staining-positive, rod-shaped and endospore-forming bacteria that represent a single species, designated strains GD05T and GD051, were isolated from a tropical forest soil and a hot spring sediment, respectively. Cells of both strains were facultatively anaerobic, catalase- and oxidase-positive, and could grow optimally at 50 °C, pH 8.0 and with 1 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence revealed that these two isolates belonged to the family Bacillaceae , but did not show sequence similarities of more than 95 % to members of other related genera. The G+C content of the genomic DNA was 43.7–44.1 mol%. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the major menaquinone was MK-7. The peptidoglycan type was A1γ (meso-diaminopimelic acid direct). On the basis of this polyphasic taxonomic analysis, the novel strains represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Sinibacillus soli gen. nov., sp. nov. is proposed. The type strain is GD05T ( = CCTCC AB 2013105T = KCTC 33117T).

Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment

A moderately halophilic bacterial strain, designated XH204T, was isolated from deep-sea sediment core (45° 58′ S 163° 11′ W) of the South Pacific Gyre during the Integrated Ocean Drilling Program Expedition 329. The strain was Gram-stain-positive, rod-shaped, motile by peritrichous flagella and produced ellipsoidal endospores subterminally positioned within swollen sporangia. Growth of strain XH204T occurred at 15–42 °C (optimum 37 °C), in the presence of 0–14 % (w/v) NaCl (optimum 4 %) and at pH 7.0–10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH204T belonged to the genus Oceanobacillus and showed the highest sequence similarity to Oceanobacillus profundus CL-MP28T (95.6 %); strain XH204T exhibited 93.4 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus Oceanobacillus , Oceanobacillus iheyensis HTE831T. The dominant fatty acids of strain XH204T were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The cell wall of strain XH204T contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose and galactose as the major whole-cell sugars. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Menaquinone-7 (MK-7) was the only isoprenoid quinone and the DNA G+C content was 38.8 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain XH204T represents a novel species of the genus Oceanobacillus , for which the name Oceanobacillus pacificus sp. nov. is proposed. The type strain is XH204T ( = DSM 25873T = JCM 18381T).

Oceanobacillus aidingensis sp. nov., a moderately halophilic bacterium

Two Gram-positive, rod-shaped moderately halophilic bacterial strains, designated AD7-25^T and AB-11, were isolated from Aiding and Manasi salt lakes in Xinjiang of China, respectively. The strains were found to be able to grow at NaCl concentrations of 0–21 % (w/v), with optimum growth occurring at 6–8 % (w/v) NaCl. The optimal temperature and pH for growth were determined to be 33–37 °C and pH 7.0–7.5. Cells of the strains are motile by means of polar flagella. Both strains can produce ellipsoidal spores. The major cellular fatty acids were identified as anteiso-C_15:0, iso-C_15:0, iso-C_14:0, anteiso-C_17:0 and iso-C_16:0. The diamino acid in the peptidoglycan and the major quinone system were determined to be meso-diaminopimelic acid (meso-DAP) and MK-7, respectively. The DNA G+C contents of stains AD7-25^T and AB-11 were 39.8 and 40.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these two novel strains are closely related to the genus Oceanobacillus showing 90–99.5 % similarity with respect to type strains. These two novel strains were most closely related to Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557^T (99.1 and 99.5 %), followed by O. oncorhynchi subsp. oncorhynchi JCM 12661^T (99.1 and 99.4 %), Oceanobacillus neutriphilus CGMCC 1.7693^T (97.0 and 97.5 %), Oceanobacillus sojae JCM 15792^T (97.6 and 98.0 %) and Oceanobacillus locisalsi KCTC 13253^T (96.5 and 96.9 %). The DNA–DNA hybridization data indicated that DNA relatedness between strains AD7-25^T and AB-11 was 91.0 %, and the genomic homology of representative strain AD7-25^T with O. oncorhynchi subsp. incaldanensis DSM 16557^T, O. oncorhynchi subsp. oncorhynchi JCM 12661^T, O. neutriphilus CGMCC 1.7693^T, O. sojae JCM 15792^T and O. locisalsi KCTC 13253^T were 41, 39, 20, 23 and 17 %, respectively. On the basis of phenotypic and phylogenetic distinctiveness, strains AD7-25^T and AB-11 should be assigned to the genus Oceanobacillus as a new species, for which the name Oceanobacillus aidingensis sp. nov. was proposed. The type strain is AD7-25^T (=CGMCC 1.9106 ^T = NBRC 105904^T).

Oceanobacillus luteolus sp. nov., isolated from soil

Two Gram-stain-positive, rod-shaped and endospore-forming bacteria, designated WM-1T and WM-4, were isolated from a paddy soil and a forest soil, respectively, in South China. Comparative 16S rRNA gene sequence analyses showed that both strains were members of the genus Oceanobacillus and most closely related to Oceanobacillus chironomi LMG 23627T with pairwise sequence similarity of 96.0%. The isolates contained menaquinone-7 (MK-7) as the respiratory quinone and anteiso-C15:0, anteiso-C17:0 and iso-C15:0 as the major fatty acids (>10%). Polar lipids consisted of a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The DNA G+C content was 38.6-39.2 mol%. The 16S rRNA gene sequence of strain WM-1T displayed 99.7 % similarity to that of strain WM-4, and DNA-DNA hybridization between the two strains showed a relatedness value of 91 %. Based on the results of this polyphasic study, strains WM-1T and WM-4 represent a novel species in the genus Oceanobacillus, for which the name Oceanobacillus luteolus sp. nov. is proposed. The type strain is WM-1T (=KCTC 33119T=CGMCC 1.12406T).

Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake

A Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain H9B(T), was isolated from a mud sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain H9B(T) were motile and produced colonies with a yellowish-grey pigment. Growth occurred between 2.5 and 10 % (w/v) NaCl and the isolate grew optimally at 7.5 % (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of pH 6-10 and 25-45 °C, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H9B(T) is a member of the genus Oceanobacillus. The closest relative to this strain was Oceanobacillus profundus CL-MP28(T) with 97.1 % 16S rRNA gene sequences similarity. The level of DNA-DNA relatedness between the novel isolate and this phylogenetically related species was 17 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid pattern of strain H9B(T) consisted of phosphatidylglycerol, diphosphatidylglycerol, four phospholipids and an aminolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 37.1 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus limi sp. nov. is proposed. The type strain of Oceanobacillus limi is strain H9B(T) ( = IBRC-M 10780(T) = KCTC 13823(T) = CECT 7997(T)).

Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov

Oceanobacillus massiliensis strain N'Diop(T) sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons.

Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye

An indigo-reducing alkaliphilic strain, designated strain N314T, was isolated from a fermented polygonum indigo (Polygonum tinctorium Lour.) liquor sample, aged for 10 months, that was obtained from Date City, Iburi Branch, Hokkaido, Japan. The 16S rRNA gene sequence phylogeny suggested that strain N314T is a member of the genus Amphibacillus , with the closest relatives being Amphibacillus indicireducens (98.9 % similarity to the type strain) and Amphibacillus xylanus (98.0 % similarity to the type strain), the only species with 16S rRNA gene sequence similarities higher than 97 % to strain N314T. The cells of the isolate stained Gram-positive and were facultatively anaerobic, straight rods that were motile by means of peritrichous flagella. The strain grew at 26–39 °C with optimum growth at 36 °C. It grew at pH 8.0–9.1, with optimum growth at pH 8.9–9.1. No isoprenoid quinone was detected, and the DNA G+C content was 38.4 mol%. The whole-cell fatty acid profile consisted mainly of iso-C15 : 0 and anteiso-C15 : 0. Analysis of DNA–DNA hybridization with the type strains of A. indicireducens and A. xylanus revealed 29±2 % and 10±2 % relatedness, respectively. Owing to differences in phenotypic characteristics from reported species of the genus A. and results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Amphibacillus iburiensis sp. nov. is proposed. The type strain is N314T ( = JCM 18529T = NCIMB 14823T).

Oceanobacillus polygoni sp. nov., a facultatively alkaliphile isolated from indigo fermentation fluid

A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SA9T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample prepared in a laboratory. The 16S rRNA gene sequence phylogeny suggested that strain SA9T was a member of the genus Oceanobacillus with the closest relative being Oceanobacillus profundus KCCM 42318T (99.3 % 16S rRNA gene sequence similarity). Cells of strain SA9T stained Gram-positive and were facultative anaerobic straight rods that were motile by peritrichous flagella. The strain grew between 5 and 48 °C (optimum, 35 °C) and at pH 7–12 (optimum, pH 9). The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 40.6±0.9 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. DNA–DNA hybridization with Oceanobacillus profundus DSM 18246T revealed a DNA–DNA relatedness value of 23±2 %. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from recognized species of the genus Oceanobacillus , strain SA9T merits classification as a representative of a novel species of the genus Oceanobacillus , for which the name Oceanobacillus polygoni sp. nov. is proposed. The type strain is SA9T ( = JCM 17252T = NCIMB 14684T). An emended description of the genus Oceanobacillus is also provided.