著者

Rajani Ghaju Shrestha Yasuhiro Tanaka Bikash Malla Sarmila Tandukar Dinesh Bhandari Daisuke Inoue Kazunari Sei Jeevan B. Sherchand Eiji Haramoto

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18052, (Released:2018-09-06)

被引用文献数

12

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Arcobacter spp. are emerging pathogens associated with gastroenteritis in humans. The objective of this study was to develop a highly sensitive and broadly reactive quantitative PCR (qPCR) assay for Arcobacter spp. and to apply the developed assay to different water sources in the Kathmandu Valley, Nepal. Fifteen samples to be analyzed by next-generation sequencing were collected from 13 shallow dug wells, a deep tube well, and a river in the Kathmandu Valley in August 2015. Among the 86 potential pathogenic bacterial genera identified, Acinetobacter, Pseudomonas, Flavobacterium, and Arcobacter were detected with relatively high abundance in 15, 14, 12, and 8 samples, respectively. A primer pair was designed with maximal nucleotide homologies among Arcobacter spp. by comparing the sequences of 16S rRNA genes. These primers were highly specific to most of the known species of Arcobacter and quantified between 1.0×101 and 6.4×106 copies reaction–1 and sometimes detected as few as 3 copies reaction–1. The qPCR assay was used to quantify Arcobacter spp. in bacterial DNA in not only the above 15 water samples, but also in 33 other samples collected from 15 shallow dug wells, 6 shallow tube wells, 5 stone spouts, 4 deep tube wells, and 3 springs. Thirteen (27%) out of 48 samples tested were positive for Arcobacter spp., with concentrations of 5.3–9.1 log copies 100 mL–1. This qPCR assay represents a powerful new tool to assess the prevalence of Arcobacter spp. in environmental water samples.

著者

Amin Mojiri Kazuma Nishimoto Takanori Awata Yoshiteru Aoi Noriatsu Ozaki Akiyoshi Ohashi Tomonori Kindaichi

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18068, (Released:2018-08-24)

被引用文献数

9

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Four salts, SEALIFE (a synthetic sea salt), NaCl, Na2SO4, and NaCl+KCl, were applied to monitor the effects of salinity on “Candidatus Scalindua sp.”, a marine anaerobic ammonium oxidation (anammox) bacterium. The highest ammonium consumption of 10 μmol mg protein–1 d–1 was observed at 88 mmol L–1 of Na in the presence of NaCl. The highest inorganic carbon uptake of 0.6 μmol mg protein–1 d–1 was observed at 117 mmol L–1 of Na and at 16 mmol L–1 of K in the presence of NaCl+KCl. Thus, Na and K are both important for maintaining a high growth rate of “Candidatus Scalindua sp.”

著者

Hui Zhu Dong Zeng Qiang Wang Ning Wang Bo Zeng Lili Niu Xueqin Ni

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17163, (Released:2018-07-25)

被引用文献数

14

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Diarrhea is often associated with marked alterations in the intestinal microbiota, termed dysbiosis; however, limited information is currently available on the intestinal microbiota in captive golden snub-nosed monkeys (Rhinopithecus roxellana) with diarrhea. We herein characterized the fecal microbiota in diarrhea and healthy monkeys using the Illumina MiSeq platform. The concentrations of fecal short-chain fatty acids (SCFAs) and copy numbers of virulence factor genes were also assessed using gas chromatography and quantitative PCR (qPCR), respectively. The results obtained showed that diarrhea monkeys harbored a distinctive microbiota from that of healthy monkeys and had 45% fewer Bacteroidetes. Among healthy subjects, old monkeys had the lowest relative abundance of Bacteroidetes. Linear discriminant analysis coupled with the effect size (LEfSe) and canonical correlation analysis (CCA) identified significant differences in microbial taxa between diarrhea and healthy monkeys. A PICRUSt analysis revealed that several pathogenic genes were enriched in diarrhea monkeys, while glycan metabolism genes were overrepresented in healthy monkeys. A positive correlation was observed between the abundance of nutrition metabolism-related genes and the individual digestive capacities of healthy monkeys. Consequently, the abundance of genes encoding heat stable enterotoxin was significantly higher in diarrhea monkeys than in healthy monkeys (P<0.05). In healthy subjects, adult monkeys had significant higher concentrations of butyrate and total SCFAs than old monkeys (P<0.05). In conclusion, the present study demonstrated that diarrhea had a microbial component and changes in the microbial structure were accompanied by altered systemic metabolic states. These results suggest that pathogens and malabsorption are the two main causes of diarrhea, which are closely related to the microbial structure and functions.

著者

Daniel Sanhueza Christine Chevillon Nicolas Bouzinbi Sylvain Godreuil Jean-François Guégan

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.2, pp.234-237, 2018 (Released:2018-07-04)

参考文献数

25

被引用文献数

7

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Species with a chitinous exoskeleton are overrepresented among the aquatic organisms carrying Mycobacterium ulcerans (MU) in nature and laboratory experiments have demonstrated the enhancing effects of chitin on the growth of MU. Field surveys identified pH as one of the key parameters delineating the distribution of MU in tropical regions. The present study investigated the relationship between chitin and pH in MU growth. By focusing on pH variations in the field, our results revealed that chitin enhanced MU growth in acidic environments. The present study provides new information on the ecological conditions favoring the development of this mycobacterium in nature.

著者

Takuro Nunoura Manabu Nishizawa Miho Hirai Shigeru Shimamura Phurt Harnvoravongchai Osamu Koide Yuki Morono Toshiaki Fukui Fumio Inagaki Junichi Miyazaki Yoshihiro Takaki Ken Takai

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17194, (Released:2018-05-25)

被引用文献数

67

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The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.

著者

Hye Young Ko Kyuseon Cho SungJun Park Jin Hwi Kim Joo-Hyon Kang Yong Seok Jeong Jong Duck Choi Yongsik Sin Cheonghoon Lee GwangPyo Ko

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17166, (Released:2018-06-01)

被引用文献数

11

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Various waterborne pathogens originate from human or animal feces and may cause severe gastroenteric outbreaks. Bacteroides spp. that exhibit strong host- or group-specificities are promising markers for identifying fecal sources and their origins. In the present study, 240 water samples were collected from two major aquaculture areas in Republic of Korea over a period of approximately 1 year, and the concentrations and occurrences of four host-specific Bacteroides markers (human, poultry, pig, and ruminant) were evaluated in the study areas. Host-specific Bacteroides markers were detected widely in the study areas, among which the poultry-specific Bacteroides marker was detected at the highest concentration (1.0–1.2 log10 copies L–1). During the sampling period, high concentrations of host-specific Bacteroides markers were detected between September and December 2015. The host-specific Bacteroides marker-combined geospatial map revealed the up-to-downstream gradient of fecal contamination, as well as the effects of land-use patterns on host-specific Bacteroides marker concentrations. In contrast to traditional bacterial indicators, the human-specific Bacteroides marker correlated with human specific pathogens, such as noroviruses (r=0.337; P<0.001). The present results indicate that host-specific Bacteroides genetic markers with an advanced geospatial analysis are useful for tracking fecal sources and associated pathogens in aquaculture areas.

著者

Kaori Ohki Kazumasa Yamada Mitsunobu Kamiya Shinya Yoshikawa

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.27, no.2, pp.171-178, 2012 (Released:2012-06-09)

参考文献数

39

被引用文献数

8 15

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Small cyanobacteria (<2 μm, pico-cyanobacteria) are abundant in waters deeper than the oxic-anoxic zone in the halocline of a saline meromictic lake, Lake Suigetsu, Fukui, Japan. We have isolated 101 strains that were grouped into six groups by means of the phycobiliprotein composition and sequence homology of the intergenic spacer between the 16S and 23S rRNA genes. Significant growth was observed under weak green light (1.5 μmol m−2 s−1, approx. 460 to 600 nm), whereas the cells died under white light at even moderate intensities. The isolates grew in a wide range of salinities (0.2 to 3.2%). Tolerance to sulfide varied: four groups grew in medium containing sulfide, however, two groups did not. None of the isolates were capable of anoxygenic photosynthetic (PS-II independent photosynthetic) growth using sulfide as an electron donor. All groups were included within fresh and brackish water of Synechococcus/Cyanobium clade, but they were not monophyletic in the 16S rRNA gene-based phylogenetic tree. The physiological properties of pico-cyanobacteria showed that they had the ability to survive in unique physicochemical environments in the halocline of this saline meromictic lake.

著者

砂村 倫成 大和田 紘一

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.13, no.1, pp.45-50, 1998-03-31 (Released:2009-10-05)

参考文献数

31

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One of the gases which scientists have so much concern related to global warming is methane. Although amounts of methane release to atmosphere from ocean and coastal areas are not so enormous compared with wetlands and rice paddies, methane stock in the sediments is considered to be big amount. It means probably that methane produced by microbial activity is oxidized and recycled also by the aerobic and anaerobic microbial activity in the sediments and waters. Unfortunately, however, quite few information is now available on the methanogenic activity related to population of methanogenic bacteria and other groups of microorganisms. In this paper, we mentioned about our study on methanogenic bacteria conducted in the Japanese coastal waters and also reviewed the studies of them which have been done in various regions.