Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7-8, 25-30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C_15 : 0 and summed feature 1 (composed of C_13 : 03-OH and/or iso-C_15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4^T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4^T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531^T (95.1 %) and Flagellimonas flava A11^T (93.9 %). Genome sequencing revealed the strain TP-CH-4^T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4^T represents a novel species of a novel genus of the family Flavobacteriaceae, for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4^T (=CGMCC 1.17120^T=KCTC 72434^T).

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture

With the increase of antimicrobial resistances due to the widespread use of antibiotics, the search of new probiotics to control aquaculture diseases has a growing public interest. The aim of this study was to isolate bacteria with antimicrobial effect from the gut of marine healthy fishes and select lactic acid bacteria (LAB) as potential probiotics, being strains considered as generally regarded as safe (GRAS) by the European Food Safety Agency (EFSA). Of a total of 45 Gram-positive strains with antimicrobial activity found in a screening of the gut microbiota of 13 marine fishes, nine were identified as LAB by 16S rRNA gene sequencing. LAB strains (five Lactococcus lactis subsp. lactis, two Enterococcus spp., one Lactobacillus plantarum, and one Leuconostoc mesenteroides subsp. mesenteroides) also showed a broad-spectrum antibacterial activity against aquaculture pathogens such as Vibrio harveyi, V. splendidus, and Photobacterium damselae and survived in experimental gastrointestinal conditions when grown in culture media modified with different values of pH and bile salts. These results showed the potential of LAB obtained from the indigenous microbiota of wild marine fishes for use as probiotics in aquaculture.

Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

BACKGROUND

Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing.

METHODS

Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com).

RESULTS

TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level.

CONCLUSIONS

TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.

Discriminative biogeochemical signatures of methanotrophs in different chemosynthetic habitats at an active mud volcano in the Canadian Beaufort Sea

Several mud volcanoes are active in the Canadian Beaufort Sea. In this study, we investigated vertical variations in methanotrophic communities in sediments of the mud volcano MV420 (420 m water depth) by analyzing geochemical properties, microbial lipids, and nucleic acid signatures. Three push cores were collected with a remotely operated vehicle from visually discriminative habitats that were devoid of megafauna and/microbial mats (DM) to the naked eye, covered with bacterial mats (BM), or colonized by siboglinid tubeworms (ST). All MV420 sites showed the presence of aerobic methane oxidation (MOx)- and anaerobic methane oxidation (AOM)-related lipid biomarkers (4α-methyl sterols and sn-2-hydroxyarchaeol, respectively), which were distinctly different in comparison with a reference site at which these compounds were not detected. Lipid biomarker results were in close agreement with 16S rRNA analyses, which revealed the presence of MOx-related bacteria (Methylococcales) and AOM-related archaea (ANME-2 and ANME-3) at the MV420 sites. 4α-methyl sterols derived from Methylococcales predominated in the surface layer at the BM site, which showed a moderate methane flux (0.04 mmol cm⁻² y⁻¹), while their occurrence was limited at the DM (0.06 mmol cm⁻² y⁻¹) and ST (0.01 mmol cm⁻² y⁻¹) sites. On the other hand, ¹³C-depleted sn-2-hydroxyarchaeol potentially derived from ANME-2 and/or ANME-3 was abundant in down-core sediments at the ST site. Our study indicates that a niche diversification within this mud volcano system has shaped distinct methanotrophic communities due to availability of electron acceptors in association with varying degrees of methane flux and bioirrigation activity.

Genotypic diversity of Streptococcus suis and the S. suis-like bacterium Streptococcus ruminantium in ruminants

Although Streptococcus suis has attracted public attention as a major swine and human pathogen, this bacterium has also been isolated from other animals, including ruminants. However, recent taxonomic studies revealed the existence of other species that were previously identified as S. suis, and some of these isolates were reclassified as the novel species Streptococcus ruminantium. In Japan, biochemically identified S. suis is frequently isolated from diseased ruminants; however, such isolates have not yet been identified accurately, and their aetiological importance in ruminants is unclear. Therefore, to understand the importance of S. suis and S. suis-like bacteria in ruminants, we reclassified S. suis isolates from ruminants according to the updated classification and investigated their genetic diversity. Although both S. suis and S. ruminantium were isolated from healthy and diseased ruminants, most of the isolates from diseased animals were S. ruminantium, implying that S. ruminantium is more likely to be associated with ruminant disease than S. suis. However, the ruminant S. suis and S. ruminantium isolates from diseased animals were classified into diverse genotypes rather than belonging to certain clonal groups. Genome sequence analysis of 20 S. ruminantium isolates provided information about the antibiotic resistance, potential virulence, and serological diversity of this species. We further developed an S. ruminantium-specific PCR assay to aid in the identification of this bacterium. The information obtained and the method established in this study will contribute to the accurate diagnosis of ruminant streptococcal infections.

Anaerotignum faecicola sp. nov., isolated from human faeces

A strictly anaerobic bacterium, designated as strain KGMB-03357^T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357^T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10-45°C (optimum temperature of 40°C) and a pH range of 5.1-10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357^T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17^T (= KCTC 15066^T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582^T, 94.9%), Anaerotignum neopropionicum DSM 03847^T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021^T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3-71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357^T are C_16:0, C_18:0, C_18∶1 cis 9, and anteiso-C_15∶0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357^T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357^T (= KCTC 15736T = DSM 107953^T).

Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi

A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium-designated as strain NKC3-5^T-was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5^T were 0.5-0.7 μm wide and 1.4-2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5-10.0 (optimum pH 9.0), and 25-40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5^T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC3-5^T clustered with bacterium Salicibibacter kimchii NKC1-1^T, with a similarity of 96.2-97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5^T and Salicibibacter kimchii NKC1-1^T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5^T. Comparative genomic analysis revealed that strain NKC3-5^T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5^T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso-C_15:0, iso-C_17:0, anteiso-C_17:0, and iso-C_15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5^T. Cell wall peptidoglycan analysis of strain NKC3-5^T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phephenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5^T (= KACC 21230^T = JCM 33437^T).

Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River

A Gram-stain-positive, aerobic, motile, and rod-shaped bacterial strain designated TGS2-1^T was isolated from sediment soil in the Nakdong River, Republic of Korea. The optimal growth of strain TGS2-1^T was observed at 28°C and pH 7.0 without NaCl supplementation. Strain TGS2-1^T revealed antibiosis against various bacteria, including Staphylococcus aureus KCCM 4051, CCARM 3089 (methicillin resistant strains), Enterococcus faecalis KCCM 11814, Escherichia coli KCTC 2443, Candida albicans KACC 7270, and Filobasidium neoformans KCTC 7902. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that strain TGS2-1^T belonged to the genus Brevibacillus and shared 93.8-99.7% sequence similarity with Brevibacillus species. Whole-genome sequencing of strain TGS2-1^T revealed a genome size of 6.2 Mbp and DNA G + C content of 47.0 mol%. The TGS2-1^T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 74.6-93.3% and 18.6-67.1%, respectively, with six related Brevibacillus genomes. The major fatty acid constituents of strain TGS2-1^T were anteiso-C_15:0 (62.3%) and anteiso-C_17:0 (10.8%). Cells of strain TGS2-1^T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, seven unidentified aminophospholipids, and five unidentified lipids. The isoprenoid quinone detected in the strain was menaquinone-7 (MK-7). Based on data obtained from this polyphasic taxonomic study, strain TGS2-1^T represents a novel species belonging to genus Brevibacillus, for which the name B. antibioticus sp. nov. is proposed. The type strain is TGS2-1^T (= KCCM 90326^T = NBRC 113840^T = FBCC-B2501).

Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

Bacterial pathogens that infect patients also contaminate hospital surfaces. These contaminants impact hospital infection control and epidemiology, prompting quantitative examination of their transmission dynamics. Here we investigate spatiotemporal and phylogenetic relationships of multidrug resistant (MDR) bacteria on intensive care unit surfaces from two hospitals in the United States (US) and Pakistan collected over one year. MDR bacteria isolated from 3.3% and 86.7% of US and Pakistani surfaces, respectively, include common nosocomial pathogens, rare opportunistic pathogens, and novel taxa. Common nosocomial isolates are dominated by single lineages of different clones, are phenotypically MDR, and have high resistance gene burdens. Many resistance genes (e.g., blaNDM, blaOXA carbapenamases), are shared by multiple species and flanked by mobilization elements. We identify Acinetobacter baumannii and Enterococcus faecium co-association on multiple surfaces, and demonstrate these species establish synergistic biofilms in vitro. Our results highlight substantial MDR pathogen burdens in hospital built-environments, provide evidence for spatiotemporal-dependent transmission, and demonstrate potential mechanisms for multi-species surface persistence.

Two novel alkaliphiles, Bacillus alkalisoli sp. nov., and Bacillus solitudinis sp. nov., isolated from saline-alkali soil

Two alkaliphilic strains, designated FJAT-45086^T and FJAT-45122^T, were isolated from alkali soli in Nima County, Tibet, China. Both strains were Gram-positive, rod-shaped and shared low 16S rRNA gene sequence similarity with the members of the genus Bacillus. They contained meso-diaminopimelic acid as the cell-wall diamino acid and MK-7 as the menaquinone. The major fatty acids (>5%) of strain FJAT-45086^T were anteiso-C_15:0, C_16:0, iso-C_15:0, C_16:1ω11c and anteiso-C_17:0, whereas strain FJAT-45122^T consisted of iso-C_15:0, anteiso-C_15:0, iso-C_17:1ω10c, iso-C_17:0, anteiso-C_17:0, C_16:0 and C16:1ω11c. The genome G + C content of strains FJAT-45086^T and FJAT-45122^T was 37.8 and 38.2 mol%, respectively. The polar lipids of strain FJAT-45086^T were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), and phosphatidyl choline (PC), whereas strain FJAT-45122^T consisted of DPG, PG, phosphatidyl methyl ethanolamine (PME) and an unidentified aminophospholipids (UAPL). The average nucleotide identity values of strains FJAT-45086^T and FJAT-45122^T were below the cut-off level (95-96%) for species delineation. Based on the results, strains FJAT-45086^T and FJAT-45122^T represent two novel species of the genus Bacillus, for which the names Bacillus alkalisoli sp. nov., and Bacillus solitudinis sp. nov., are proposed. The type strain, FJAT-45122^T (=DSM 104631^T = CCTCC AB 2016254^T), FJAT-45086^T (=DSM 104056^T = CCTCC AB 2016232^T).

Space Station conditions are selective but do not alter microbial characteristics relevant to human health

The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.

Thermus caldilimi sp. nov., a thermophilic bacterium isolated from a geothermal area

A Gram-stain negative, aerobic bacterium, designated strain YIM 78456^T, was isolated from a hot spring sediment, Ngamring county, Tibet, south-west China. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was found to be aerobic and rod-shaped. Colonies were observed to be pale yellow and circular. The strain was found to grow at pH 7.0-8.0 (optimum, pH 7.0), 45-65 °C (optimum, 55 °C) and in the presence of up to 1.5% NaCl. Comparison of the 16S rRNA gene sequence of strain YIM 78456^T and other members of the genus Thermus showed sequence similarities ranging from 90.3 to 97.3%, with strain YIM 78456^T showing close sequence similarity to Thermus caliditerrae YIM 77925^T (97.3%). The phylogenetic trees based on 16S rRNA gene sequences showed that strain YIM 78456^T forms a distinct clade with T. caliditerrae YIM 77925^T. The predominant menaquinone was identified as MK-8 and the DNA G+C content was determined to be 65.1 mol%. The major cellular fatty acids (> 10%) were identified as iso-C_15:0, anteiso-C_15:0 and iso-C_17:0. The polar lipids were found to consist of an aminophospholipid, a phospholipid and glycolipids. On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, it is proposed that strain YIM 78456^T represents a novel species of the genus Thermus, for which the name Thermus caldilimi sp. nov. is proposed. The type strain is YIM 78456^T (= KCTC 52948^T = NBRC 113036^T).

Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample

A novel strain, YIM 131921^T, was isolated from a Physcia sp. lichen collected from the South Bank Forest of the Baltic Sea. The strain is Gram-negative, catalase positive and oxidase negative, strictly aerobic, asporogenous, non-motile and reddish brown in colour. The temperature and pH for growth were found to be 20-30 °C (optimum 28 °C) and pH 6.5-12.0 (optimum pH 7.0 ± 0.5). No growth was observed in the presence of NaCl. Based on 16S rRNA gene sequence similarity, strain YIM 131921^T shares high similarities with Rubellimicrobium roseum YIM 48858^T (98.3%), followed by Rubellimicrobium mesophilum MSL-20^T (96.8%), Rubellimicrobium aerolatum 5715S-9^T (96.1%) and Rubellimicrobium thermophilum DSM 16684^T (96.0%). Phylogenetic trees showed YIM 131921^T forms a cluster with type strains of the genus Rubellimicrobium. The predominant cellular fatty acids (> 20%) were identified as summed feature 8 (C_18:1ω7c) and C_16:0. Q-10 was found to be the predominant respiratory ubiquinone. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, glycolipid, phospholipids and an unidentified aminolipid. The DNA G + C content of the draft genome sequence is 66.6 mol%. Strain YIM 131921^T showed an average nucleotide identity value of 80.3% and a digital DNA-DNA hybridizations value of 26.1% with the reference strain R. roseum YIM 48858^T based on draft genome sequences. Based on comparative analyses of phenotypic, molecular, chemotaxonomic data and genomic comparisons, strain YIM 131921^T is concluded to represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium rubrum sp. nov. is proposed. The type strain is YIM 131921^T (= CGMCC 1.13958^T = NBRC 114054^T = KCTC 72461^T).

Mucilaginibacter terrigena sp. nov. sp., A Novel Member of the Family Sphingobacteriaceae

A bacterial strain, 17JY9-4^T, was isolated from a soil sample collected on Jeju Island, South Korea. Colonies grown on R2A agar are pale pink in color, and cells are Gram-stain negative, short, and rod-shaped. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus Mucilaginibacter in the family Sphingobacteriaceae, with high levels of 16S rRNA sequence similarity shared with Mucilaginibacter lutimaris BR-3^T (98.0%), Mucilaginibacter rigui WPCB133^T (98.0%), Mucilaginibacter phyllosphaerae PP-F2F-G21^T (97.0%), Mucilaginibacter amnicola TAPP7^T (96.8%), and Mucilaginibacter soli R9-65^T (96.7%). Growth of strain 17JY9-4^T occurs at 10-30 °C, pH 6-8, and in the presence of 0-1.0% NaCl. The genomic G+C content is 44.38 mol%. The predominant respiratory quinone of the isolate is MK-7; the major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c) (39.7%), iso-C_15:0 (22.8%), iso-C_17:0 3-OH (7.8%), and C_16:0 (7.7%); and the major polar lipid is phosphatidylethanolamine. The phenotypic and chemotaxonomic data support the placement of strain 17JY9-4^T within the genus Mucilaginibacter. However, the DNA-DNA relatedness between the isolate and M. rigui, M. lutimaris, M. phyllosphaerae, M. amnicola, and M. soli were 44.3 ± 3.0%, 38.6 ± 3.7%, 23.2 ± 2.9%, 21.9 ± 3.1%, and 18.6 ± 3.7%, respectively. The results of 16S rRNA gene sequence similarity analysis, DNA-DNA hybridization analysis, and the observed differentiating phenotypic properties from other closely related taxa clearly indicate that strain 17JY9-4^T represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter terrigena sp. nov. is proposed. The type strain is 17JY9-4^T (= KCTC 62294^T = JCM 33049^T).

Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail

A Gram-stain positive, short rod-shaped, aerobic, motile by means of gliding, yellow-pigmented actinobacterium, designated strain DD4a^T, was isolated from dry yellow foxtail. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DD4a^T is closely related to Amnibacterium soli MB78^T (98.4% similarity), Amnibacterium kyonggiense KSL51201-037^T (98.2%) and Amnibacterium endophyticum 1T4Z-3^T (97.43%). Strain DD4a^T forms yellow colonies on R2A agar medium. The peptidoglycan was found to contains diaminopimelic acid (which is a diagnostic cell wall diamino acid), alanine, glutamic acid and lysine. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids and an unidentified polar lipid were found to be present in strain DD4a^T. The major cellular fatty acids anteiso-C_15:0 (42.9%) and iso-C_16:0 (34.6%) were found in strain DD4a^T. The predominant respiratory quinones were found to be MK-11 and MK-12. The DNA G+C content of strain DD4a^T is 73.9 mol%. DNA-DNA relatedness of strain DD4a^T with A. soli MB78^T, A. kyonggiense KSL51201-037^T, and A. endophyticum 1T4Z-3^T were 53.3% (± 1.1%), 47.0% (± 0.5%), and 47.9% (± 0.9%), respectively. The digital DNA-DNA hybridisation and average nucleotide identity values between strain DD4a^T and A. kyonggiense KSL51201-037^T were determined to be 26.1% and 82.7%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, DD4a^T represents a novel member of the genus Amnibacterium, for which the name Amnibacterium setariae sp. nov., is proposed. The type strain of Amnibacterium setariae is DD4a^T (= KACC 19817^T = JCM 32878^T).

Comparative Analysis of Draft Genome Sequence of Rhodococcus sp. Eu-32 with Other Rhodococcus Species for Its Taxonomic Status and Sulfur Metabolism Potential

Rhodococcus sp. Eu-32 has shown an extended novel dibenzothiophene desulfurization sulfur-specific 4S pathway and could remove significant amounts of organic sulfur from coal. Here, we present the draft genome sequence of Eu-32 with a genome size of approximately 5.61 Mb, containing 5065 protein coding sequences with a G+C content of 65.1%. The Rhodococcus sp. Eu-32 showed ~ 99% identity at the 16S rRNA gene sequence level while < 34% digital DNA-DNA hybridization and < 81% average nucleotide identity values with the genome sequence of most closely related known Rhodococcus species, suggesting that it is taxonomically different from the already reported Rhodococcus species. Among the annotated genes, 90 are involved in the metabolism of sulfur. Comparative genome analysis suggests many commonalities in sulfur metabolism gene sets that may have evolved due to many factors including ecological pressures. Our study and the genome sequence data will be available for further research and will provide insights into potential biotechnological and industrial applications of this bacterium.

Corallincola luteus sp. nov., a marine bacterium isolated from surface sediment of Bohai Sea of China

A novel Gram-stain negative, strictly aerobic, rod-shaped motile bacterium with a single flagellum, designated strain DASS28^T, was isolated from surface sediment of Bohai Sea in China. Growth occurred in the presence of 1.0-4.0% NaCl (w/v, optimum 2.0%), at 10-37 °C (optimum 20 °C) on the Marine agar 2216E and pH 6.0-10.0 (optimum pH 8.0). The major fatty acids (> 10% of total fatty acids) were summed feature 3 (C_16:1ω7c and/or iso-C_15:0 2-OH), C_16:0 and C_18:1ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and two unidentified polar lipids. The major respiratory quinone was ubiquinone-8 (Q-8). The genomic DNA G + C content calculated from the genome sequence of strain DASS28^T was 48.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain DASS28^T belongs to the genus Corallincola and shows high 16S rRNA gene sequence similarity of 96.7% to Corallincola platygyrae JLT 2006^T (= JCM18796^T = CGMCC 1.10992^T). On the basis of the polyphasic evidence, strain DASS28^T is considered to represent a novel species in the genus Corallincola, for which the name Corallincola luteus sp. nov. is proposed. The type strain is DASS28^T (= KCTC 52376^T = MCCC 1K03208^T).

Flavobacterium sangjuense sp. nov. isolated from sediment

A yellow-pigmented bacterial strain, GS03^T, was isolated from sediment in a branch of the Nackdong River in Sangju, Korea. Cells were observed to be Gram-negative, aerobic and rod-shaped with gliding motility, and to be positive for catalase and oxidase. Growth was found to occur at 4-30 °C (optimum 25 °C), at pH 7.0-8.5 (optimum pH 7.5) and at NaCl 0% (optimum NaCl 0%, w/v). The major cellular fatty acids (> 10% of the total) were identified as iso C_15:0, iso C_15:1 G, C_15:1ω6c, iso C_15: 0 3-OH and iso C_17: 0 3-OH. The major respiratory quinone was found to be menaquinone MK-6. The genome sequence of GS03^T is 3.1 Mb with G+C content of 36.1 mol%. The major polar lipids of the isolate were identified as phosphatidylethanolamine, three unidentified aminolipids, two unidentified phospholipids, an unidentified lipid and an unidentified aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GS03^T clusters with Flavobacterium paronense KNUS1T^T, with similarity of 96.8%. The phenotypic, phylogenetic, and chemotaxonomic characteristics indicate that strain GS03^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium sangjuense sp. nov. is proposed. The type strain is GS03^T (= FBCC 502459^T = KCTC 62568^T = JCM 32764^T).

iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis

BACKGROUND

One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking.

RESULTS

We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline.

CONCLUSIONS

The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae)

The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter

A Gram-stain-positive, rod-shaped, non-endospore-forming motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13ar^T was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13ar^T belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88^T (98.5%), Paenibacillus hordei RH-N24^T (98.4%) and Paenibacillus nicotianae YIM h-19^T (98.1%). The major fatty acid was anteiso-C_15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13ar^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13ar^T (= KACC 18728^T = NBRC 112013^T).

Identification of the predominant microbiota during production of lait caillé, a spontaneously fermented milk product made in Burkina Faso

The spontaneously fermented curdled milk product from Burkina Faso, lait caillé is prepared by traditional processing from raw unpasteurised milk. The fermentation lasts 1-3 days. This study aims to identify the predominant microbiota involved in lait caillé fermentation from cow milk. A survey on lait caillé end-products from local markets showed pH ranges of 3.5 to 4.2. Counts of total lactic acid bacteria (LAB) were 7.8 ± 0.06 to 10.0 ± 0.03 log CFU/g and yeast counts were 5.3 ± 0.06 to 8.7 ± 0.01 log CFU/g, together with considerate amounts of Enterobacteriaceae < 3.00 to 8.4 ± 0.14 log CFU/g. Sampling throughout the entire fermentation of lait caillé was performed at a traditional house-hold production site. A drop in pH from 6.7 ± 0.01 at 0 h to 4.3 ± 0.08 in the end-product (59 h) was found. Total LAB counts increased to 8.6 ± 0.02 log CFU/g in the end-product, while yeast and Enterobacteriaceae counts reached 6.4 ± 0.11 and 6.7 ± 0.00 log CFU/g, respectively. LAB and yeasts isolated during the fermentation were clustered by (GTG)₅ repetitive-PCR fingerprinting followed by 16S and 26S rRNA gene sequencing, respectively. Microbial successions were observed with Leuconostoc mesenteroides being the predominant LAB followed by Pediococcus pentosaceus and Weissella paramesenteroides at the onset, while Lactococcus lactis and Enterococcus spp. where the predominant LAB after 7 h of fermentation. During the first 18 h Candida parapsilosis was the dominant yeast species, while from 35 h to the end-product, Saccharomyces cerevisiae predominated. The microbial safety risk pointed out in this study, showed the need for implementation of good manufacturing practices including pasteurisation and use of well-defined starter cultures.

Paenibacillus lutimineralis sp. nov., Isolated From Bentonite

Strain MBLB1234^T was isolated from bentonite samples collected at Guryong mining area located in Pohang, Republic of Korea and was taxonomically characterized by a polyphasic approach. This strain was a Gram-stain-negative, motile, endospore-forming, facultative anaerobic, catalase-positive, oxidase-negative, and rod-shaped bacterium. Strain MBLB1234^T was able to grow at 20‒45 °C (optimum, 37 °C), pH 6.0‒10.0 (optimum, 7.0-8.0), and 0‒5.0% (w/v) NaCl (optimum, 0.5%). Genome size was 6,497,679 bp with a G + C content of 46.4 mol %. The genome was predicted to contain 5233 protein-coding genes, and 135 rRNA genes consisted of 10 5S rRNAs, 10 16S rRNAs, 10 23S rRNAs, and 105 tRNAs. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain MBLB1234^T clustered with Paenibacillus motobuensis JCM 12774^T and P. aceti JCM 31170^T with 98.3-98.5% and 97.2-97.4% sequencing similarity, respectively. The major fatty acids of strain MBLB1234^T were anteiso-C_15:0 (35.7%), anteiso-C_17:0 (17.8%), iso-C_17:0 (14.5%), and C_16:0 (11.0%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, and one unidentified phospholipid, six unidentified aminophospholipids, and one unidentified lipid. The predominant isoprenoid quinone was menaquinone-7. DNA-DNA hybridization values between strain MBLB1234^T and P. motobuensis JCM 12774^T and P. aceti JCM 31170^T were 34 and 38%, respectively. Average nucleotide identity value between strains MBLB1234^T and P. aceti L14^T was 82.3%. Based on characteristics of genomic, phenotypic, chemotaxonomic, and phylogenetic analyses, strain MBLB1234^T represents a novel species of the genus P. , for which the name P. lutimineralis sp. nov. is proposed. The type strain is MBLB1234^T (= JCM 32684^T = KCTC 33978^T).

Flavisolibacter galbus sp. nov., isolated from soil in Jeju Island

A Gram-stain negative, non-motile, and yellow-coloured bacterium, designated 17J28-26^T, was isolated from soil in Jeju Island, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 17J28-26^T formed a distinct lineage within the family Chitinophagaceae (order Chitinophagales, class Chitinophagia), and is closely related to Flavisolibacter ginsenosidimutans (96.8% 16S rRNA gene sequence similarity), and Flavisolibacter ginsengisoli (96.6%). Growth was observed at 18-37 °C (optimum 30 °C) in R2A medium at pH 7.0. The major cellular fatty acids of strain 17J28-26^T were summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and iso-C_15:0. The predominant respiratory quinone was MK-7. The major polar lipid was identified as phosphatidylethanolamine. Based on biochemical, chemotaxonomic and phylogenetic characteristics, strain 17J28-26^T represents a novel bacterial species within the family Chitinophagaceae, for which the name Flavisolibacter galbus sp. nov. is proposed. The type strain of Flavisolibacter galbus is 17J28-26^T (= KCTC 62222^T = JCM 33203^T).

Description of Halegenticoccus soli gen. nov., sp. nov., a halophilic archaeon isolated from a soil sample of Ebi lake

Two extreme halophilic archaeal strains, SYSUA9-0^T and SYSUA9-1, were isolated from Ebi lake of Xinjiang, China. The colonies were Gram-negative, coccoid, and non-motile. Strains were aerobic and grew at 25-50 °C (optimum at 37 °C), in the presence of 10-35% (w/v) NaCl (optimum at 20-22%), and pH 6.0-8.0 (optimum at 7.0). The 16S rRNA gene sequence result revealed that the two strains were closely related to Haloprofundus marisrubri SB9^T (92.7% similarity). The DNA-DNA hybridization value (97% ± 1%) suggested that SYSUA9-0^T and SYSUA9-1 were similar; however, their sequence similarities with other archaeal members suggested that they were novel candidates. The genomic G + C content of SYSUA9-0^T was 66.9%. The average nucleotide identity value between SYSU A9-0^T and Haloprofundus marisrubri SB9^T was 69.1%, which was far below the cutoff value (95-96%) proposed to define the species boundary. The polar lipids were phosphatidylglycerol (PG), phosphatidylglycerolphosphate methylester (PGP-Me), sulfated mannosyl glucosyl diether, mannosyl glucosyldiether, and four unidentified glycolipids. Phenotypic, chemotaxonomic and comparative genome analysis suggested that SYSU A9-0^T and SYSU A9-1 represent a novel species of a new genus within the family Haloferacaceae, for which the name Halegenticoccus soli gen. nov., sp. nov., is proposed. The type strain is SYAUA9-0^T (= KCTC4241^T = CGMCC 1.15765^T).

Ottowia flava sp. nov., isolated from fish intestines

A novel Gram-negative bacterium, non-motile and short rod-shaped, designated strain GY511^T, was isolated from the intestines of fish collected from Maowei Sea, China. Growth occurred at pH 6.0-9.0 (optimum 7.0), 4-37 °C (optimum 28 °C) and at 0-2.5% (w/v) NaCl (optimum 1.0%). The result of 16S rRNA gene sequence analysis showed that strain GY511^T is closely related to O. oryzae NBRC 113109^T (97.6%), O. konkukae DSM 105395^T (97.4%), Ottowia beijingensis CGMCC 1.12324^T (95.9%), Ottowia pentelensis DSM 21699^T (95.2%) and Ottowia thiooxydans DSM 14619^T (95.0%). The DNA-DNA hybridization values of strain GY511^T with O. oryzae NBRC 113109^T and O. konkukae DSM 105395^T were 35.4 ± 3.1% and 26.3 ± 1.8%, respectively. The major fatty acids (> 10%) were identified as summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0 and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, two unidentified aminolipids and an unidentified phospholipid. The G+C content of the genomic DNA was 62.9 mol%. Thiosulfate could be utilized as co-substrate for aerobic growth and was oxidised to sulfate. On the basis of phenotypic, chemotaxonomic and molecular data, strain GY511^T is considered to represent a novel species of the genus Ottowia, for which the name Ottowia flava sp. nov. is proposed. The type strain is GY511^T (= NBRC 113500^T = DSM 107425^T = CGMCC 1.13650^T).

Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp

A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604^T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604^T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604^T was the most closely related to P. koreensis Ch05^T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604^T and P. koreensis Ch05^T, P. alcaliphilus DSM 8512^T, and P. stylophorae KTW-16^T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA-4604^T was observed at 10-40°C (optimum, 37°C), pH 6.0-10.0 (optimum, pH 7.0), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0-2.0%). Strain CBA4604^T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C_18:1ω7c/C_18:1ω6c) and C_18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA-4604^T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604^T (= KACC 19579^T = JCM 32510^T).

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.

Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation

BACKGROUND

Consuming red and processed meat has been associated with an increased risk of colorectal cancer (CRC), which is partly attributed to exposure to carcinogens such as heterocyclic amines (HCA) formed during cooking and preservation processes. The interaction of gut microbes and HCA can result in altered bioactivities and it has been shown previously that human gut microbiota can transform mutagenic HCA to a glycerol conjugate with reduced mutagenic potential. However, the major form of HCA in the colon are glucuronides (HCA-G) and it is not known whether these metabolites, via stepwise microbial hydrolysis and acrolein conjugation, are viable precursors for glycerol conjugated metabolites. We hypothesized that such a process could be concurrently catalyzed by bacterial beta-glucuronidase (B-GUS) and glycerol/diol dehydratase (GDH) activity. We therefore investigated how the HCA-G PhIP-N2-β-D-glucuronide (PhIP-G), a representative liver metabolite of PhIP (2-Amino-1-methyl-6-phenylimidazo [4,5-b] pyridine), which is the most abundant carcinogenic HCA in well-cooked meat, is transformed by enzymatic activity of human gut microbial representatives of the phyla Firmicutes, Bacteroidetes, and Proteobacteria.

RESULTS

We employed a combination of growth and enzymatic assays, and a bioanalysis approach combined with metagenomics. B-GUS of Faecalibacterium prausnitzii converted PhIP-G to PhIP and GDH of Flavonifractor plautii, Blautia obeum, Eubacterium hallii, and Lactobacillus reuteri converted PhIP to PhIP-M1 in the presence of glycerol. In addition, B-GUS- and GDH-positive bacteria cooperatively converted PhIP-G to PhIP-M1. A screen of genes encoding B-GUS and GDH was performed for fecal microbiome data from healthy individuals (n = 103) and from CRC patients (n = 53), which revealed a decrease in abundance of taxa with confirmed GDH and HCA transformation activity in CRC patients.

CONCLUSIONS

This study for the first time demonstrates that gut microbes mediate the stepwise transformation of PhIP-G to PhIP-M1 via the intermediate production of PhIP. Findings from this study suggest that targeted manipulation with gut microbes bearing specific functions, or dietary glycerol supplementation might modify gut microbial activity to reduce HCA-induced CRC risk.

Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula

A Gram-stain-positive, oxidase- and catalase-positive motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5^T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5^T was observed at 15-37°C (optimum 30°C) on R2A broth, pH 6.0-8.0 (optimum 7.0), and 0-5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5^T was most closely related to Arthrobacter silviterrae KIS14-16^T, Arthrobacter livingstonensis LI2^T, Arthrobacter stackebrandtii CCM 2783^T, Arthrobacter cryoconiti Cr6-08^T, Arthrobacter ramosus CCM 1646^T, and Arthrobacter psychrochitiniphilus GP3^T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5^T was 64.7 mol%, and its DNA-DNA relatedness values with A. silviterrae KIS14-16^T, A. livingstonensis LI2^T, A. stackebrandtii CCM 2783^T, A. psychrochitiniphilus GP3^T, A. ramosus CCM 1646^T, and A. cryoconiti Cr6-08^T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H₂) and major fatty acids were anteiso-C_15:0, anteiso-C_17:0, iso-C_15:0, and iso-C_16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5^T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5^T (= KCTC 49189^T = LMG 31284^T).

Mesorhizobium composti sp. nov., isolated from compost

A polyphasic taxonomic approach was used to characterize a presumptively novel diazotrophic bacterium, designated strain CC-YTH430^T, isolated from a compost sample in Taiwan. Cells of strain CC-YTH430^T were found to be Gram-stain negative, facultative anaerobic rods that formed yellow-colored colonies on nutrient agar. Cell growth occurred at 15-40 °C, pH 5.0-9.0 and in the presence of 0-2% NaCl. Strain CC-YTH430^T resembled Mesorhizobium species while sharing high pair-wise 16S rRNA gene sequence similarities with Mesorhizobium silamurunense, Mesorhizobium thiogangeticum, Mesorhizobium plurifarium, Mesorhizobium tamadayense, Mesorhizobium amorphae (96.9% each), Mesorhizobium sediminum (96.8%), and Mesorhizobium soli (96.5%) and < 96.5% similarity to other species. Strain CC-YTH430^T showed 78.8-79.7% average nucleotide identity compared to the type strains of M. amorphae, M. plurifarium, M. soli, M. tamadayense and M. wenxiniae. The N₂-fixing activity of strain CC-YTH430^T was 0.2 nmol ethylene h^-1 at 30 °C. The respiratory system was ubiquinone 10 (Q-10) and the DNA G+C content was 62.0 ± 0.2 mol%. The major fatty acids (> 5%) were C_16:0, C_17:0 cyclo, C_19:0 cyclo ω8c, C_14:0 3OH/C_16:1 iso I and C_18:1ω7c/C_18:1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and an unidentified aminolipid in major amounts. In addition, phosphatidylethanolamine, an unidentified lipid and several unidentified polar lipids were also found in moderate-to-trace amounts. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-YTH430^T is proposed to represent a novel Mesorhizobium species, for which the name Mesorhizobium composti sp. nov. (type strain CC-YTH430^T = BCRC 81024^T = JCM 31762^T) is proposed.

Development of a novel cultivation technique for uncultured soil bacteria

In this study, a new diffusion bioreactor was developed to cultivate hidden bacterial communities in their natural environment. The newly developed method was investigated to cultivate microbial communities from the forest soil, and the results were evaluated against traditional culture methods and compared to the results of a pyrosequencing-based molecular survey. The molecular analysis revealed that a diverse bacterial population was present in the soil sample. However, both the newly developed method and the traditional method recovered more than 400 isolates, which belonged to only four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Although these isolates were distributed over only four major phyla, the use of the newly developed technique resulted in the successful cultivation of 35 previously uncultured strains, whereas no such strains were successfully cultivated by the traditional method. Furthermore, the study also found that the recovery of uncultured bacteria and novel isolates was related to sampling season, incubation period, and cultivation media. The use of soil collected in summer, a prolonged incubation period, and low-substrate modified media increased the recovery of uncultured and novel isolates. Overall, the results indicate that the newly designed diffusion bioreactor can mimic the natural environment, which permits the cultivation of previously uncultured bacteria.

Gut microbiota and butyrate level changes associated with the long-term administration of proton pump inhibitors to old rats

The association between adverse effects of PPI and gut microbiota in old age has yet to be elucidated. We assessed changes in the gut microbiota and butyrate levels following the long-term administration of PPIs to old rats and investigated their associations. F344 aged male rats were fed a PPI-supplemented diet for 50 weeks. The ileal microbiota was analysed by metagenomic sequencing of the 16S rRNA, while the butyrate concentration was measured by high-performance liquid chromatography. We observed a significant decrease in microbial diversity following PPI administration in the 2-year-old rats but not in the 74-week-old rats. PPI treatment reduced both commensal bacteria and opportunistic pathogens, particularly in the 2-year-old rats. Enterotypes comprising the majority of the control samples were enriched in Lactobacillus, while other enterotypes in the PPI group were dominated by Turicibacter or Romboutsia. The PPI treatment reduced the butyrate concentrations in the intestines and colons of 74-week-old rats compared to the control group. The abundance of Lactobacillus significantly correlated with butyrate concentrations in 74-week-old rats. In conclusion, long-term administration of PPIs alters the gut microbiota and butyrate concentrations in rats, particularly in old age, which may be an underlying mechanism of PPI-induced adverse effects such as pseudomembranous colitis.