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Zhang Y, An J, Yang G, Zhang X, Xie Y, Chen L, Feng Y. Structure features of GH10 xylanase from Caldicellulosiruptor bescii: implication for its thermophilic adaption and substrate binding preference. Acta Biochim Biophys Sin (Shanghai) 2016; 48:948-957. [PMID: 27563004 DOI: 10.1093/abbs/gmw086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic species of organisms known to date. In our previous study, GH10 xylanase CbXyn10B from C. bescii displayed outstanding hydrolytic activity toward various xylans at high temperatures. To understand the structural basis for this protein's catalysis and thermostability, we solved the crystal structures of CbXyn10B and its complexes with xylooligosaccharides. These structural models were used to guide comparison with its mesophilic counterpart PbXyn10B. A distinctive structural feature is that thermophilic CbXyn10B presents a relatively stable interaction between the extended loops L7 and L8 in the catalytic cleft by an extensive hydrogen bonding network, which is mediated by Lys306, Arg314 and three well-ordered water molecules. Moreover, a unique aromatic cluster consisting of Try17, Phe20, Phe21, and Phe337 may enhance the interaction between the N- and C- terminus. Targeted mutagenesis demonstrated that these interactions substantially contribute to enzyme stabilization, as indicated by a considerable decrease in the melting temperature (Tm) of CbXyn10B by substituting critical residues with Ala. Therefore, it was shown that not only the aromatic interaction connecting protein termini but also the extensive hydrogen bonding network formed between surface loops could restrict the local structural flexibility and contribute significantly to the overall stability of enzymes. Furthermore, the xylooligosaccharides were found to tightly bind to the glycone subsites of xylanase, indicating higher affinities at these subsites and reflecting its substrate binding preference. Our results suggest that CbXyn10B is stabilized with distinct rigidity at the catalytic cleft as well as the terminal regions, which provides insights into the evolutionary strategy for accommodating the functional needs of GH10 enzymes to high temperature.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Sheng P, Huang J, Zhang Z, Wang D, Tian X, Ding J. Construction and Characterization of a Cellulolytic Consortium Enriched from the Hindgut of Holotrichia parallela Larvae. Int J Mol Sci 2016; 17:ijms17101646. [PMID: 27706065 PMCID: PMC5085679 DOI: 10.3390/ijms17101646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 11/16/2022] Open
Abstract
Degradation of rice straw by cooperative microbial activities is at present the most attractive alternative to fuels and provides a basis for biomass conversion. The use of microbial consortia in the biodegradation of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, and so on. In this study, a cellulolytic microbial consortium was enriched from the hindgut of Holotrichia parallela larvae via continuous subcultivation (20 subcultures in total) under static conditions. The degradation ratio for rice straw was about 83.1% after three days of cultivation, indicating its strong cellulolytic activity. The diversity analysis results showed that the bacterial diversity and richness decreased during the consortium enrichment process, and the consortium enrichment process could lead to a significant enrichment of phyla Proteobacteria and Spirochaetes, classes Clostridia, Epsilonproteobacteria, and Betaproteobacteria, and genera Arcobacter, Treponema, Comamonas, and Clostridium. Some of these are well known as typical cellulolytic and hemicellulolytic microorganisms. Our results revealed that the microbial consortium identified herein is a potential candidate for use in the degradation of waste lignocellulosic biomass and further highlights the hindgut of the larvae as a reservoir of extensive and specific cellulolytic and hemicellulolytic microbes.
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Affiliation(s)
- Ping Sheng
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Jiangli Huang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Zhihong Zhang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Dongsheng Wang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Xiaojuan Tian
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Jiannan Ding
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
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203
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Tiwari S, Sarangi BK, Thul ST. Identification of arsenic resistant endophytic bacteria from Pteris vittata roots and characterization for arsenic remediation application. J Environ Manage 2016; 180:359-65. [PMID: 27257820 DOI: 10.1016/j.jenvman.2016.05.029] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 05/09/2023]
Abstract
Mitigation of arsenic (As) pollution is a topical environmental issue of high R&D priority. The present investigation was carried out to isolate As resistant endophytes from the roots of Indian ecotype Pteris vittata and characterize their As transformation and tolerance ability, plant growth promoting characteristics and their role to facilitate As uptake by the plant. A total of 8 root endophytes were isolated from plants grown in As amended soil (25 mg As kg(-1)). These isolates were studied for minimum inhibitory concentration (MIC), arsenite As(III) - arsenate As(V) transformation ability, plant growth promoting (PGP) characteristics through siderophore, indole acetic acid (IAA) production, phosphatase, ACC deaminase activity, and presence of arsenite oxidase (aox) and arsenite transporter (arsB) genes. On the basis of 16S rDNA sequence analysis, these isolates belong to Proteobacteria, Firmicutes and Bacteroidetes families under the genera Bacillus, Enterobacter, Stenotrophomonas and Rhizobium. All isolates were found As tolerant, of which one isolates showed highest tolerance up to 1000 mg L(-1) concentration in SLP medium. Five isolates were IAA positive with highest IAA production up to 60 mg/L and two isolates exhibited siderophore activity. Phosphatase activity was shown by only one isolate while ACC deaminase activity was absent in all the isolates. The As transformation study by silver nitrate test showed that only two strains had dual characteristics of As(III) oxidation and As (V) reduction, four strains exhibited either of the characteristics while other two didn't confirmed any of the two characteristics. Presence of aox gene was detected in two strains and arsB gene in six isolates. The strain with highest As tolerance also showed highest IAA production and occurrence of arsB gene. Present investigation may open up further scope of utilizing these endophytes for up gradation of phytoextraction process.
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Affiliation(s)
- Sarita Tiwari
- National Environmental Engineering Research Institute, Council of Scientific and Industrial Research, Nehru Marg, Nagpur 440020, India
| | - Bijaya Ketan Sarangi
- National Environmental Engineering Research Institute, Council of Scientific and Industrial Research, Nehru Marg, Nagpur 440020, India.
| | - Sanjog T Thul
- National Environmental Engineering Research Institute, Council of Scientific and Industrial Research, Nehru Marg, Nagpur 440020, India
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204
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Kashkak ES, Bel'kova NL, Danilova EV, Dagurova OP, Namsaraev BB, Gorlenko VM. Phylogenetic and Functional Prokaryotic Diversity in the Hoito-Gol Mesothermal Mineral Spring (Eastern Savan Mountains. Buryat Renuhlie). Mikrobiologiia 2016; 85:555-567. [PMID: 29364603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing was used for comparative analysis of microbial communities of the water and mat from the Hoito-Gol mesothermal mineral sulfide spring (Eastern Sayan Mountains, Buryat Republic). Activity of microbial communities was determined. While both spring biotopes were dominated by members of three bacterial phyla, Proteobacteria, Bacteroidetes, and Firmicutes, they differed drastically in the composition of predominant phylotypes (at the genus level). In the water, the organisms wide spread in aquatic'environments were predominant, mostly aerobic chemoorganotrophs of the generaAcinetobacter, Pe- dobacter, and Flavobacterium. In the microbial mat,;the organisms actively involved in the sulfur cycle predominated, including sulfur-reducing bacteria Sulfurospirillum, sulfate-reducing deltaproteobacteria, sulfur- oxidizing chemoautotrophic bacteria, anoxygenic phototrophic bacteria of,the phyla Chloroflexi and Chloro- bi, as well as purple bacteria belonging to the Q-, P--, and y-Proteobacteria. Microbial mats of the spring exhibited higher phylogenetic diversity compared to high-temperature mats containing photosynthetic microorganisms.
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205
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Galach'yants AD, Bel'kova NL, Sukhanova EV, Romanovskaya VA, Gladka GV, Bedoshvili ED, Parfenova VV. [Diversity and Physiological and Biochemical Properties of Heterotrophic Bacteria. Isolated from Lake Baikal Neuston.]. Mikrobiologiia 2016; 85:568-579. [PMID: 29364604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
For heterotrophic microorganisms (44 strains) isolated-from the surface film of Lake Baikal, iden- tification was carried out and their. physiological and biochemical characteristics were determined. Com- pared to the water column, diversity of cultured heterotrophs was low, indicating formation of stable micro- bial communities at the air-water interphase interface. Heterotrophic bacteria isolated from the surface mi- crolayer exhibited the enzymatic activity comparable to that for strains form other biofilm associations. Deinococcusfi6us strain NA202 'vas the most active component of the community, capable of utilization of the broadest spectrum of mono- and disaccharides,'sugars, and amino acids. This strain possessed the highest diversity of extracellular enzymes and was the most resistant to UV radiation. The physiological and bio- chemical properties of this strain may-be responsible for its adaptation to survival in extreme conditions of the surface microlayer. Our results improve our understanding of occurrence of UV-resistant strains in freshwater ecosystems.
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206
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Dong S, Wang Y, Ji J, Zheng J. [Heterologous expression and characterization of a thermostable acylCoA synthetase]. Wei Sheng Wu Xue Bao 2016; 56:1477-1485. [PMID: 29738220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE An acyl-CoA synthetase (ACS) was characterized by in vitro biochemical assays to get a potential biocatalyst for the generation of polyketide precursors such as propionyl-CoA and butyryl-CoA. METHODS An ACS was identified in Caldicellulosiruptor owensensis OL genome by BLAST program using malonyl-CoA synthetase as the query sequence. The enzyme was heterologously expressed in Escherichia coli cells and purified to homogeneity by affinity purification. In vitro biochemical assays were used to reveal the substrate profile, the optimum reaction condition, the stability and the kinetics of the enzyme while the site-directed mutagenesis was used to assay the function of active site residues. RESULTS The enzyme was promiscuous enough to accept propionic acid, butyric acid, 2-methyl-propionic acid, pentanoic acid, 2-methyl-butyric acid, 3-methyl-butyric acid and cyclohexanecarboxylic acid as the substrates. It was most active at 30℃ and pH 7.0 and relatively stable because 45% activity remained after 8 hours incubation at 70℃. Interestingly, the substrate specificity of the enzyme could be switched by engineering three residues of active site. CONCLUSION The ACS from C. owensensis OL was a potential biocatalyst for the generation of polyketide precursors.
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207
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Eichmiller JJ, Hamilton MJ, Staley C, Sadowsky MJ, Sorensen PW. Environment shapes the fecal microbiome of invasive carp species. Microbiome 2016; 4:44. [PMID: 27514729 PMCID: PMC4981970 DOI: 10.1186/s40168-016-0190-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/02/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. RESULTS We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. CONCLUSIONS The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.
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Affiliation(s)
- Jessica J. Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
| | - Matthew J. Hamilton
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Christopher Staley
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Michael J. Sadowsky
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Peter W. Sorensen
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
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208
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He Q, Zhou J, Wang H, Zhang J, Wei L. Microbial population dynamics during sludge granulation in an A/O/A sequencing batch reactor. Bioresour Technol 2016; 214:1-8. [PMID: 27115745 DOI: 10.1016/j.biortech.2016.04.088] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/11/2016] [Accepted: 04/16/2016] [Indexed: 06/05/2023]
Abstract
The evolution of the bacterial population during formation of denitrifying phosphorus removal granular sludge was investigated using high-throughput pyrosequencing. As a result, mature granules with a compact structure were obtained in an anaerobic/aerobic/anoxic (A/O/A) sequencing batch reactor under an organic loading rate as low as 0.3kg COD/(m(3)·d). Rod-shaped microbes were observed to cover with the outer surface of granules. Besides, reliable COD and simultaneous nitrogen and phosphorus removal efficiencies were achieved over the whole operation period. MiSeq pyrosequencing analysis illustrated that both the microbial diversity and richness increased sharply during the granulation process, whereas they stayed stable after the presence of granules. Some microorganisms seemed to contribute to the formation of granules, and some were identified as functional bacterial groups responsible for constructing the biological reactor.
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Affiliation(s)
- Qiulai He
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Jun Zhou
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China.
| | - Jing Zhang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Li Wei
- State Key Lab of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090, China
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209
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Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome 2016; 4:38. [PMID: 27391224 PMCID: PMC4939015 DOI: 10.1186/s40168-016-0183-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease. Cynomolgous macaques were infected with the SIV-HIV chimeric virus SHIV89.6P. Bronchoalveolar lavage fluid samples were collected pre-infection and every 4 weeks for 53 weeks post-infection. The microbiota was characterized at each time point by 16S ribosomal RNA (rRNA) sequencing. RESULTS We observed individual variation in the composition of the lung microbiota with a proportion of the macaques having Tropheryma whipplei as the dominant organism in their lungs. Bacterial communities varied over time both within and between animals, but there did not appear to be a systematic alteration due to SHIV infection. Development of obstructive lung disease in the SHIV-infected animals was characterized by a relative increase in abundance of oral anaerobes. Network analysis further identified a difference in community composition that accompanied the development of obstructive disease with negative correlations between members of the obstructed and non-obstructed groups. This emphasizes how species shifts can impact multiple other species, potentially resulting in disease. CONCLUSIONS This study is the first to investigate the dynamics of the lung microbiota over time and in response to immunosuppression in a non-human primate model. The persistence of oral bacteria in the lung and their association with obstruction suggest a potential role in pathogenesis. The lung microbiome in the non-human primate is a valuable tool for examining the impact of the lung microbiome in human health and disease.
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Affiliation(s)
- Alison Morris
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Joseph N. Paulson
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
- />Present address: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- />Present address: Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Hisham Talukder
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Laura Tipton
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Heather Kling
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Lijia Cui
- />Tsinghua University School of Medicine, Beijing, China
| | - Adam Fitch
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Mihai Pop
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Karen A. Norris
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Elodie Ghedin
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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210
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Benucci GMN, Bonito GM. The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales. Microb Ecol 2016; 72:4-8. [PMID: 27026101 DOI: 10.1007/s00248-016-0755-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/18/2016] [Indexed: 06/05/2023]
Abstract
Fungi that produce their fruiting bodies underground within the soil profile are known commonly as truffles. Truffle fruiting bodies harbor a diverse but poorly understood microbial community of bacteria, yeasts, and filamentous fungi. In this study, we used next-generation 454 amplicon pyrosequencing of the V1 and V4 region of the bacterial 16S ribosomal DNA (rDNA) in order to characterize and compare effects of truffle species and geographic origin on the truffle microbiome. We compared truffle microbiomes of the glebal tissue for eight truffle species belonging to four distinct genera within the Pezizales: Tuber, Terfezia, Leucangium, and Kalapuya. The bacterial community within truffles was dominated by Proteobacteria, Bacterioides, Actinobacteria, and Firmicutes. Bacterial richness within truffles was quite low overall, with between 2-23 operational taxonomic units (OTUs). Notably, we found a single Bradyrhizobium OTU to be dominant within truffle species belonging to the genus Tuber, irrespective of geographic origin, but not in other truffle genera sampled. This study offers relevant insights into the truffle microbiome and raises questions concerning the recruitment and function of these fungal-associated bacteria consortia.
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Affiliation(s)
- Gian Maria Niccolò Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.
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211
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Chen L, Luo Y, Xu J, Yu Z, Zhang K, Brookes PC. Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation. Microb Ecol 2016; 72:240-251. [PMID: 27079454 DOI: 10.1007/s00248-016-0766-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Previous investigations observed that when soil was fumigated with ethanol-free CHCl3 for 24 h and then incubated under appropriate conditions, after the initial flush of CO2 was over, soil organic carbon (SOC) mineralization continued at the same rate as in the non-fumigated soil. This indicates that, following fumigation, the much diminished microbial population still retained the same ability to mineralize SOC as the much larger non-fumigated population. We hypothesize that although fumigation drastically alters the soil bacterial community abundance, composition, and diversity, it has little influence on the bacterial C-metabolic functions. Here, we conducted a 30-day incubation experiment involving a grassland soil and an arable soil with and without CHCl3 fumigation. At days 0, 7, and 30 of the incubation, the bacterial abundances were determined by quantitative PCR, and the bacterial community composition and diversity were assessed via the 16S rRNA gene amplicon sequencing. PICRUSt was used to predict the metagenome functional content from the sequence data. Fumigation considerably changed the composition and decreased the abundance and diversity of bacterial community at the end of incubation. At day 30, Firmicutes (mainly Bacilli) accounted for 70.9 and 94.6 % of the total sequences in the fumigated grassland and arable soil communities, respectively. The two fumigated soil communities exhibited large compositional and structural differences during incubation. The families Paenibacillaceae, Bacillaceae, and Symbiobacteriaceae dominated the bacterial community in the grassland soil, and Alicyclobacillaceae in the arable soil. Fumigation had little influence on the predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of the main acid esters, saccharides, amino acids, and lipids in the grassland soil community. The saccharide-metabolizing KO abundances were decreased, but the acid ester- and fatty acid-metabolizing KO abundances were elevated by fumigation in the arable soil community. Our study suggests functional redundancy regarding the bacterial genetic potential associated with SOC mineralization.
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Affiliation(s)
- Lin Chen
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhuyun Yu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Kaile Zhang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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212
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Ou JY, Huang JQ, Song Y, Yao SW, Peng XC, Wang MF, Ou SY. Feruloylated Oligosaccharides from Maize Bran Modulated the Gut Microbiota in Rats. Plant Foods Hum Nutr 2016; 71:123-128. [PMID: 27165128 DOI: 10.1007/s11130-016-0547-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Corn bran is a byproduct produced from corn milling; it is rich in ferulic acid and hemicellulose. In this research, the effects of feruloylated oligosaccharides (FOs) from maize bran on the microbial diversity and profiles in rat feces were investigated through 16S rRNA sequencing. FOs significantly increased bacterial richness and diversity compared with the control and xylooligosaccharides (XOS) alone. In comparison with the control group and the group administrated with XOS, FOs orally administered at 300 mg/kg increased OTU in feces by 57.0 and 24.8 %, and Chao value by 93.4 and 37.6 %, respectively. FOs also influenced obesity- and diabetes-associated bacteria. Oral administration of FOs at 300 mg/kg decreased the ratio of Firmicutes to Bacteroidetes from 477.7:1 to 55.1:1; greatly increased the reads of bacteria that were previously found resistant against diabetes in rats, such as Actinobacteria, Bacteroides, and Lactobacillus; whereas decreased diabetes-prone bacteria, such as Clostridium and Firmicutes.
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Affiliation(s)
- Juan-Ying Ou
- Food and Nutritional Science Program, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jun-Qing Huang
- Institute of Integrated Chinese and Western Medicine, Medical College of Jinan University, Guangzhou, 510632, China
| | - Yuan Song
- Institute of Integrated Chinese and Western Medicine, Medical College of Jinan University, Guangzhou, 510632, China
| | - Sheng-Wen Yao
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xi-Chun Peng
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Ming-Fu Wang
- Food and Nutritional Science Program, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Shi-Yi Ou
- Department of Food Science and Engineering, Jinan University, Guangzhou, Guangdong, 510632, China.
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213
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He Z, Hu Y, Yin Z, Hu Y, Zhong H. Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria. Environ Manage 2016; 57:1319-1328. [PMID: 26894618 DOI: 10.1007/s00267-016-0675-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
Three soil samples obtained from different sites adjacent to a chromium slag heap in a steel alloy factory were taken to examine the effect of chromium contamination on soil bacterial diversity as determined by construction of 16S rDNA clone libraries and sequencing of selected clones based on restriction fragment length polymorphism (RFLP) analysis. Results revealed that Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Alphaproteobacteria occurred in all three soil samples, although the three samples differed in their total diversity. Sample 1 had the highest microbial diversity covering 12 different classes, while Sample 3 had the lowest microbial diversity. Strains of six different species were successfully isolated, one of which was identified as Zobellella denitrificans. To our knowledge, this is the first report of a strain belonging to the genus Zobellella able to resist and reduce chromium. Among all isolates studied, Bacillus odysseyi YH2 exhibited the highest Cr(VI)-reducing capability, with a total removal of 23.5 % of an initial Cr(VI) concentration of 350 mg L(-1).
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Affiliation(s)
- Zhiguo He
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China.
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, Hunan, 410083, People's Republic of China.
| | - Yuting Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, Hunan, 410083, People's Republic of China
| | - Zhen Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, Hunan, 410083, People's Republic of China
| | - Yuehua Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, Hunan, 410083, People's Republic of China
| | - Hui Zhong
- School of Life Science, Central South University, Changsha, Hunan, 410012, People's Republic of China
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214
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Rôças IN, Alves FRF, Rachid CTCC, Lima KC, Assunção IV, Gomes PN, Siqueira JF. Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis. PLoS One 2016; 11:e0154653. [PMID: 27135405 PMCID: PMC4852894 DOI: 10.1371/journal.pone.0154653] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
This study used a next-generation sequencing approach to identify the bacterial taxa occurring in the advanced front of caries biofilms associated with pulp exposure and irreversible pulpitis. Samples were taken from the deepest layer of dentinal caries lesions associated with pulp exposure in 10 teeth diagnosed with symptomatic irreversible pulpitis. DNA was extracted and the microbiome was characterized on the basis of the V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. Bacterial taxa were mapped to 14 phyla and 101 genera composed by 706 different OTUs. Three phyla accounted for approximately 98% of the sequences: Firmicutes, Actinobacteria and Proteobacteria. These phyla were also the ones with most representatives at the species level. Firmicutes was the most abundant phylum in 9/10 samples. As for genera, Lactobacillus accounted for 42.3% of the sequences, followed by Olsenella (13.7%), Pseudoramibacter (10.7%) and Streptococcus (5.5%). Half of the samples were heavily dominated by Lactobacillus, while in the other half lactobacilli were in very low abundance and the most dominant genera were Pseudoramibacter, Olsenella, Streptococcus, and Stenotrophomonas. High bacterial diversity occurred in deep dentinal caries lesions associated with symptomatic irreversible pulpitis. The microbiome could be classified according to the relative abundance of Lactobacillus. Except for Lactobacillus species, most of the highly prevalent and abundant bacterial taxa identified in this study have been commonly detected in infected root canals. The detected taxa can be regarded as candidate pathogens for irreversible pulpitis and possibly the pioneers in pulp invasion to initiate endodontic infection.
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Affiliation(s)
- Isabela N. Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
| | - Flávio R. F. Alves
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
- * E-mail:
| | - Caio T. C. C. Rachid
- Institute of Microbiology Prof. Paulo de Góes, Federal University of Rio de Janeiro, RJ, Brazil
| | - Kenio C. Lima
- Department of Preventive Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Isauremi V. Assunção
- Department of Preventive Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Patrícia N. Gomes
- Department of Preventive Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - José F. Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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215
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Kasparovska J, Pecinkova M, Dadakova K, Krizova L, Hadrova S, Lexa M, Lochman J, Kasparovsky T. Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows. PLoS One 2016; 11:e0154642. [PMID: 27124615 PMCID: PMC4849651 DOI: 10.1371/journal.pone.0154642] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/15/2016] [Indexed: 01/04/2023] Open
Abstract
In this study, we compared the effects of two diets containing different isoflavone concentrations on the isoflavone transfer from feed into milk and on the rumen microbiota in lactating dairy cows. The on-farm experiment was conducted on twelve lactating Czech Fleckvieh x Holstein cows divided into two groups, each with similar mean milk yield. Twice daily, cows were individually fed a diet based on maize silage, meadow hay and supplemental mixture. Control group (CTRL) received the basal diet while the experimental group (EXP) received the basal diet supplemented with 40% soybean isoflavone extract. The average daily isoflavone intake in the EXP group (16 g/day) was twice as high as that in the CTRL group (8.4 g/day, P<0.001). Total isoflavone concentrations in milk from the CTRL and EXP groups were 96.89 and 276.07 μg/L, respectively (P<0.001). Equol concentrations in milk increased from 77.78 μg/L in the CTRL group to 186.30 μg/L in the EXP group (P<0.001). The V3-4 region of bacterial 16S rRNA genes was used for metagenomic analysis of the rumen microbiome. The experimental cows exhibited fewer OTUs at a distance level of 0.03 compared to control cows (P<0.05) and reduced microbial richness compared to control cows based on the calculated Inverse Simpson and Shannon indices. Non-metric multidimensional scaling analysis showed that the major contributor to separation between the experimental and control groups were changes in the representation of bacteria belonging to the phyla Bacteroidetes, Proteobacteria, Firmicutes, and Planctomycetes. Surprisingly, a statistically significant positive correlation was found only between isoflavones and the phyla Burkholderiales (r = 0.65, P<0.05) and unclassified Betaproteobacteria (r = 0.58, P<0.05). Previous mouse and human studies of isoflavone effects on the composition of gastrointestinal microbial populations generally report similar findings.
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Affiliation(s)
- Jitka Kasparovska
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martina Pecinkova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Katerina Dadakova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ludmila Krizova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sylvie Hadrova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Matej Lexa
- Department of Information Technologies, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Kasparovsky
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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216
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Zanphorlin LM, de Giuseppe PO, Honorato RV, Tonoli CCC, Fattori J, Crespim E, de Oliveira PSL, Ruller R, Murakami MT. Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. Sci Rep 2016; 6:23776. [PMID: 27029646 PMCID: PMC4815018 DOI: 10.1038/srep23776] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/01/2015] [Indexed: 12/26/2022] Open
Abstract
Psychrophilic enzymes evolved from a plethora of structural scaffolds via multiple molecular pathways. Elucidating their adaptive strategies is instrumental to understand how life can thrive in cold ecosystems and to tailor enzymes for biotechnological applications at low temperatures. In this work, we used X-ray crystallography, in solution studies and molecular dynamics simulations to reveal the structural basis for cold adaptation of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. We discovered that the selective pressure of low temperatures favored mutations that redesigned the protein surface, reduced the number of salt bridges, exposed more hydrophobic regions to the solvent and gave rise to a tetrameric arrangement not found in mesophilic and thermophilic homologues. As a result, some solvent-exposed regions became more flexible in the cold-adapted tetramer, likely contributing to enhance enzymatic activity at cold environments. The tetramer stabilizes the native conformation of the enzyme, leading to a 10-fold higher activity compared to the disassembled monomers. According to phylogenetic analysis, diverse adaptive strategies to cold environments emerged in the GH1 family, being tetramerization an alternative, not a rule. These findings reveal a novel strategy for enzyme cold adaptation and provide a framework for the semi-rational engineering of β-glucosidases aiming at cold industrial processes.
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Affiliation(s)
| | - Priscila Oliveira de Giuseppe
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Rodrigo Vargas Honorato
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Juliana Fattori
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Elaine Crespim
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Roberto Ruller
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
| | - Mario Tyago Murakami
- Brazilian Biosciences National Laboratory from the National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
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217
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Wang Q, Qian L, Jiang S, Cai C, Ma D, Gao P, Li H, Jiang K, Tang M, Hou J, Liu J, Cui W. Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology. PLoS One 2016; 11:e0150937. [PMID: 26966911 PMCID: PMC4788350 DOI: 10.1371/journal.pone.0150937] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
The neo (neomycin phosphotransferase) gene is widely used as a selection marker in the production of genetically engineered animals and plants. Recent attention has been focused on safety concerns regarding neo transgene expression. In this study, neo transgenic and non-transgenic piglets were randomly assigned into Group A and Group B to evaluate effects of neo transgene by studying changes in gut microbiota using high-throughput sequencing. Group A pigs were fed a standard diet supplemented with antibiotic neomycin; Group B pigs were fed a standard diet. We examined horizontal transfer of exogenous neo gene using multiplex PCR; and investigated if the presence of secreted NPT II (neo expression product) in the intestine could lead to some protection against neomycin in transgenic pigs by monitoring different patterns of changes in gut microbiota in Group A animals. The unintended effects of neo transgene on gut microbiota were studied in Group B animals. Horizontal gene transfer was not detected in gut microbiota of any transgenic pigs. In Group A, a significant difference was observed between transgenic pigs and non-transgenic pigs in pattern of changes in Proteobacteria populations in fecal samples during and post neomycin feeding. In Group B, there were significant differences in the relative abundance of phyla Firmicutes, Bacteroidetes and Proteobacteria, and genera Lactobacillus and Escherichia-Shigella-Hafnia between transgenic pigs and non-transgenic pigs. We speculate that the secretion of NPT II from transgenic tissues/cells into gut microbiota results in the inhibition of neomycin activity and the different patterns of changes in bacterial populations. Furthermore, the neo gene also leads to unintended effects on gut microbiota in transgenic pigs that were fed with basic diet (not supplemented with neomycin). Thus, our data in this study caution that wide use of the neo transgene in genetically engineered animals should be carefully considered and fully assessed.
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Affiliation(s)
- Qingqing Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
| | - Lili Qian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, P R China
| | - Shengwang Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
| | - Chunbo Cai
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, P R China
| | - Dezun Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
| | - Pengfei Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Qingdao University of Science & Technology, Qingdao, 266042, P R China
| | - Hegang Li
- Institute of Animal Sciences, Qingdao, 266100, P R China
| | - Ke Jiang
- Institute of Animal Sciences, Qingdao, 266100, P R China
| | - Maoxue Tang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
| | - Jian Hou
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, P R China
| | - Jie Liu
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Qingdao University of Science & Technology, Qingdao, 266042, P R China
| | - Wentao Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P R China
- * E-mail:
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218
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Cardinali-Rezende J, Rojas-Ojeda P, Nascimento AMA, Sanz JL. Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology. Chemosphere 2016; 146:519-525. [PMID: 26741558 DOI: 10.1016/j.chemosphere.2015.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/09/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Biomethanization entails a good means to reduce the organic fraction (OF) derived from municipal solid wastes (MSW). The bacterial diversity of a full scale MSW anaerobic reactor located in Madrid (Spain) was investigated using high-throughput 454 pyrosequencing. Even though the proteolytic bacteria prevailed throughout all of the process, community shifts were observed from the start-up to the steady-state conditions, with an increasing biodiversity displayed over time. The Bacteroidetes and the Firmicutes were the majority phyla: 55.1 and 40.2% (start-up) and 18.7 and 78.7 (steady-state) of the total reads. The system's lack of evenness remains noteworthy as the sequences affiliated to the proteolytic non-saccharolytic Proteiniphylum, Gallicola and Fastidiosipila genera, together with the saccharolytic Saccharofermentans, were predominant on the system and this predominance appears to correlate with the presence of a high ammonium concentration. The 454 pyrosequencing revealed a great diversity of rare organisms which seemingly do not sustain any metabolic roles in the course of the OF-MSW degradation. However, this scarce and unique microbiota can confer great resilience to the system as a buffer against nutritional and environmental changing conditions, thus opening the door to increase the current knowledge about the bacterial community dynamics taking place during MSW treatment processes.
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Affiliation(s)
- Juliana Cardinali-Rezende
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain; Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31.270-901, Brazil
| | - Patricia Rojas-Ojeda
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31.270-901, Brazil
| | - José L Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain.
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219
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Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Rep 2016; 14:2142-2153. [PMID: 26923597 DOI: 10.1016/j.celrep.2016.02.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 12/20/2022] Open
Abstract
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
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Affiliation(s)
- Andres Gomez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Liberec Zoo, Liberec 460 01, Czech Republic
| | - Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Klara Vlckova
- Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - David Modry
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic; CEITEC, Central European Institute for Technology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - Angelique Todd
- Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic
| | | | - Melissa J Remis
- Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA
| | | | - Elise Morton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Juan D Umaña
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA
| | - H Rex Gaskins
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Brenda A Wilson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rebecca M Stumpf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bryan A White
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven R Leigh
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
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220
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Huang X, Liu L, Wen T, Zhang J, Wang F, Cai Z. Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation. Appl Microbiol Biotechnol 2016; 100:5581-93. [PMID: 26875875 DOI: 10.1007/s00253-016-7362-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 01/23/2016] [Accepted: 01/26/2016] [Indexed: 11/26/2022]
Abstract
Reductive soil disinfestation (RSD) has been proven to be an effective and environmentally friendly way to control many soilborne pathogens and diseases. In this study, the RSDs using ethanol (Et-RSD) and alfalfa (Al-RSD) as organic carbons were performed in a Rhizoctonia solani-infected soil, and the dissimilarities of microbial communities during the RSDs and after planting two seasons of cucumber seedlings in the RSDs-treated soil were respectively investigated by MiSeq pyrosequencing. The results showed that, as for bacteria, Coprococcus, Flavisolibacter, Rhodanobacter, Symbiobacterium, and UC-Ruminococcaceae became the dominant bacterial genera at the end of Al-RSD. In contrast, Et-RSD soil involved more bacteria belonging to Firmicutes, such as Sedimentibacter, UC-Gracilibacteraceae, and Desulfosporosinus. For fungi, Chaetomium significantly increased at the end of RSDs, while Rhizoctonia and Aspergillus significantly decreased. After planting two seasons of cucumber seedlings, those bacteria belonging to Firmicutes significantly decreased, but Lysobacter and Rhodanobacter belonging to the phylum Proteobacteria as well as UC-Sordariales and Humicola belonging to Ascomycota alternatively increased in Al- and Et-RSD-treated soils. Besides, some nitrification, denitrification, and nitrogen fixation genes were apparently increased in the RSD-treated soils, but the effect was more profound in Al-RSD than Et-RSD. Overall, Et-RSD could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms (Lysobacter and Rhodanobacter) and further improve nitrogen transformation activities in the soil at the coming cropping season.
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Affiliation(s)
- Xinqi Huang
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
- Key Laboratory of Virtual Geographical Environment (VGE), Ministry of Education, Nanjing Normal University, Nanjing, 210023, China
| | - Liangliang Liu
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
| | - Teng Wen
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jinbo Zhang
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
- Key Laboratory of Virtual Geographical Environment (VGE), Ministry of Education, Nanjing Normal University, Nanjing, 210023, China
| | - Fenghe Wang
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
| | - Zucong Cai
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China.
- Key Laboratory of Virtual Geographical Environment (VGE), Ministry of Education, Nanjing Normal University, Nanjing, 210023, China.
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Gloux K, Anba-Mondoloni J. Unique β-Glucuronidase Locus in Gut Microbiomes of Crohn's Disease Patients and Unaffected First-Degree Relatives. PLoS One 2016; 11:e0148291. [PMID: 26824357 PMCID: PMC4732671 DOI: 10.1371/journal.pone.0148291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/15/2016] [Indexed: 12/24/2022] Open
Abstract
Crohn's disease, an incurable chronic inflammatory bowel disease, has been attributed to both genetic predisposition and environmental factors. A dysbiosis of the gut microbiota, observed in numerous patients but also in at least one hundred unaffected first-degree relatives, was proposed to have a causal role. Gut microbiota β-D-glucuronidases (EC 3.2.1.33) hydrolyse β-D-glucuronate from glucuronidated compounds. They include a GUS group, that is homologous to the Escherichia coli GusA, and a BG group, that is homologous to metagenomically identified H11G11 BG and has unidentified natural substrates. H11G11 BG is part of the functional core of the human gut microbiota whereas GusA, known to regenerate various toxic products, is variably found in human subjects. We investigated potential risk markers for Crohn's disease using DNA-sequence-based exploration of the β-D-glucuronidase loci (GUS or Firmicute H11G11-BG and the respective co-encoded glucuronide transporters). Crohn's disease-related microbiomes revealed a higher frequency of a C7D2 glucuronide transporter (12/13) compared to unrelated healthy subjects (8/32). This transporter was in synteny with the potential harmful GUS β-D-glucuronidase as only observed in a Eubacterium eligens plasmid. A conserved NH2-terminal sequence in the transporter (FGDFGND motif) was found in 83% of the disease-related subjects and only in 12% of controls. We propose a microbiota-pathology hypothesis in which the presence of this unique β-glucuronidase locus may contribute to an increase risk for Crohn's disease.
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Affiliation(s)
- Karine Gloux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- * E-mail:
| | - Jamila Anba-Mondoloni
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Abstract
Human intestinal flora comprises thousands of bacterial species. Growth and composition of intestinal microbiota is dependent on various parameters, including immune mechanisms, dietary factors and intestinal motility. Patients with spinal cord injury (SCI) frequently display neurogenic bowel dysfunction due to the absence of central nervous system control over the gastrointestinal system. Considering the bowel dysfunction and altered colonic transit time in patients with SCI, we hypothesized the presence of a significant change in the composition of their gut microbiome. The objective of this study was to characterize the gut microbiota in adult SCI patients with different types of bowel dysfunction. We tested our hypothesis on 30 SCI patients (15 upper motor neuron [UMN] bowel syndrome, 15 lower motor neuron [LMN] bowel syndrome) and 10 healthy controls using the 16S rRNA sequencing. Gut microbial patterns were sampled from feces. Independent of study groups, gut microbiota of the participants were dominated by Blautia, Bifidobacterium, Faecalibacterium and Ruminococcus. When we compared all study groups, Roseburia, Pseudobutyrivibrio, Dialister, Marvinbryantia and Megamonas appeared as the genera that were statistically different between groups. In comparison to the healthy group, total bacterial counts of Pseudobutyrivibrio, Dialister and Megamonas genera were significantly lower in UMN bowel dysfunction group. The total bacterial count of Marvinbryantia genus was significantly lower in UMN bowel dysfunction group when compared to the LMN group. Total bacterial counts of Roseburia, Pseudobutyrivibrio and Megamonas genera were significantly lower in LMN bowel dysfunction group when compared to healthy groups. Our results demonstrate for the first time that butyrate-producing members are specifically reduced in SCI patients when compared to healthy subjects. The results of this study would be of interest since to our knowledge, microbiome-associated studies targeting SCI patients are non-existent and the results might help explain possible implications of gut microbiome in SCI.
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Affiliation(s)
- Bilgi Gungor
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Emre Adiguzel
- Department of PMR, Gulhane Military Medical Academy, Turkish Armed Forces Rehabilitation Center, Ankara,Turkey
| | - Ihsan Gursel
- THORLAB, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Bilge Yilmaz
- Department of PMR, Gulhane Military Medical Academy, Turkish Armed Forces Rehabilitation Center, Ankara,Turkey
- * E-mail: (MG); (BY)
| | - Mayda Gursel
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
- * E-mail: (MG); (BY)
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Hervé V, Junier T, Bindschedler S, Verrecchia E, Junier P. Diversity and ecology of oxalotrophic bacteria. World J Microbiol Biotechnol 2016; 32:28. [PMID: 26748805 DOI: 10.1007/s11274-015-1982-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/16/2015] [Indexed: 11/27/2022]
Abstract
Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.
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Affiliation(s)
- Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Eric Verrecchia
- Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
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Shin KC, Choi HY, Seo MJ, Oh DK. Compound K Production from Red Ginseng Extract by β-Glycosidase from Sulfolobus solfataricus Supplemented with α-L-Arabinofuranosidase from Caldicellulosiruptor saccharolyticus. PLoS One 2015; 10:e0145876. [PMID: 26710074 PMCID: PMC4692446 DOI: 10.1371/journal.pone.0145876] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Ginsenoside compound K (C-K) is attracting a lot of interest because of its biological and pharmaceutical activities, including hepatoprotective, antitumor, anti-wrinkling, and anti-skin aging activities. C-K has been used as the principal ingredient in skin care products. For the effective application of ginseng extracts to the manufacture of cosmetics, the PPD-type ginsenosides in ginseng extracts should be converted to C-K by enzymatic conversion. For increased yield of C-K from the protopanaxadiol (PPD)-type ginsenosides in red-ginseng extract (RGE), the α-L-arabinofuranoside-hydrolyzing α-L-arabinofuranosidase from Caldicellulosiruptor saccharolyticus (CS-abf) was used along with the β-D-glucopyranoside/α-L-arabinopyranoside-hydrolyzing β-glycosidase from Sulfolobus solfataricus (SS-bgly) because SS-bgly showed very low hydrolytic activity on the α-L-arabinofuranoside linkage in ginsenosides. The optimal reaction conditions for C-K production were as follows: pH 6.0, 80°C, 2 U/mL SS-bgly, 3 U/mL CS-abf, and 7.5 g/L PPD-type ginsenosides in RGE. Under these optimized conditions, SS-bgly supplemented with CS-abf produced 4.2 g/L C-K from 7.5 g/L PPD-type ginsenosides in 12 h without other ginsenosides, with a molar yield of 100% and a productivity of 348 mg/L/h. To the best of our knowledge, this is the highest concentration and productivity of C-K from ginseng extract ever published in literature.
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Affiliation(s)
- Kyung-Chul Shin
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hye-Yeon Choi
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Ju Seo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
- * E-mail:
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225
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Cheng Y, Fox S, Pemberton D, Hogg C, Papenfuss AT, Belov K. The Tasmanian devil microbiome-implications for conservation and management. Microbiome 2015; 3:76. [PMID: 26689946 PMCID: PMC4687321 DOI: 10.1186/s40168-015-0143-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/08/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Tasmanian devil, the world's largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has established an insurance population, which currently holds over 600 devils in captive facilities across Australia. Microbes are known to play a crucial role in the health and well-being of humans and other animals, and increasing evidence suggests that changes in the microbiota can influence various aspects of host physiology and development. To improve our understanding of devils and facilitate management and conservation of the species, we characterised the microbiome of wild devils and investigated differences in the composition of microbial community between captive and wild individuals. RESULTS A total of 1,223,550 bacterial 16S ribosomal RNA (rRNA) sequences were generated via Roche 454 sequencing from 56 samples, including 17 gut, 15 skin, 18 pouch and 6 oral samples. The devil's gut microbiome was dominated by Firmicutes and showed a high Firmicutes-to-Bacteroidetes ratio, which appears to be a common feature of many carnivorous mammals. Metabolisms of carbohydrates, amino acids, energy, cofactors and vitamins, nucleotides and lipids were predicted as the most prominent metabolic pathways that the devil's gut flora contributed to. The microbiota inside the female's pouch outside lactation was highly similar to that of the skin, both co-dominated by Firmicutes and Proteobacteria. The oral microbiome had similar proportions of Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. CONCLUSIONS Compositional differences were observed in all four types of microbiota between devils from captive and wild populations. Certain captive devils had significantly lower levels of gut bacterial diversity than wild individuals, and the two groups differed in the proportion of gut bacteria accounting for the metabolism of glycan, amino acids and cofactors and vitamins. Further studies are underway to investigate whether alterations in the microbiome of captive devils can have impacts on their ability to adapt and survive following re-introduction to the wild.
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Affiliation(s)
- Yuanyuan Cheng
- Faculty of Veterinary Science, RMC Gunn Building, University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Samantha Fox
- Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, Tasmania, 7000, Australia.
| | - David Pemberton
- Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, Tasmania, 7000, Australia.
| | - Carolyn Hogg
- Zoo and Aquarium Association, Mosman, New South Wales, 2088, Australia.
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, RMC Gunn Building, University of Sydney, Sydney, New South Wales, 2006, Australia.
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Pershina E, Valkonen J, Kurki P, Ivanova E, Chirak E, Korvigo I, Provorov N, Andronov E. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems. PLoS One 2015; 10:e0145072. [PMID: 26684619 PMCID: PMC4684275 DOI: 10.1371/journal.pone.0145072] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/28/2015] [Indexed: 02/01/2023] Open
Abstract
One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.
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Affiliation(s)
- Elizaveta Pershina
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Saint-Petersburg State University, Saint-Petersburg, Russia
- * E-mail:
| | - Jari Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Päivi Kurki
- Natural Resources Institute Finland, Mikkeli, Finland
| | - Ekaterina Ivanova
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Laboratory of biology and biochemistry of soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Evgeny Chirak
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Ilia Korvigo
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nykolay Provorov
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny Andronov
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Saint-Petersburg State University, Saint-Petersburg, Russia
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Liebensteiner MG, Pinkse MWH, Nijsse B, Verhaert PDEM, Tsesmetzis N, Stams AJM, Lomans BP. Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes. Environ Microbiol Rep 2015; 7:936-945. [PMID: 26332065 DOI: 10.1111/1758-2229.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
This study reports the ability of one hyperthermophilic and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. Aeropyrum pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in Ae. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with the observations made on Ar. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.
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Affiliation(s)
- Martin G Liebensteiner
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Martijn W H Pinkse
- Analytical Biotechnology Section, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
- Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Peter D E M Verhaert
- Analytical Biotechnology Section, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
- Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, TX, 77082, USA
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Bart P Lomans
- Shell Global Solutions International B.V., Kessler Park 1, 2288 GS, Rijswijk, The Netherlands
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228
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Shirey TB, Dykes JK, Lúquez C, Maslanka SE, Raphael BH. Characterizing the fecal microbiota of infants with botulism. Microbiome 2015; 3:54. [PMID: 26593441 PMCID: PMC4655454 DOI: 10.1186/s40168-015-0119-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Infant botulism is the most prevalent form of botulism in the USA, representing 68.5 % of cases reported from 2001-2012. Infant botulism results when botulinum toxin-producing clostridia (BTPC) colonize the infant gut with concomitant in vivo production of the highly potent botulinum neurotoxin (BoNT). The gut microbiota of infants with botulism is largely uncharacterized; therefore, it remains unclear whether the microbiota profile of these patients are distinct in composition, abundance, or diversity. To address this uncertainty, we employed 16S rRNA gene profiling to characterize the fecal microbiota in 14 stool samples among laboratory-confirmed and non-confirmed infant botulism cases. RESULTS Seven bacterial phyla were identified among all 14 infant stool samples examined. Compared to samples from non-confirmed cases, the fecal microbiota of infant botulism patients displayed significantly higher Proteobacteria abundance. Of the 20 bacterial families identified, Enterobacteriaceae was significantly more abundant in samples from infants with botulism. Firmicutes abundance and the abundance ratio of Firmicutes/Proteobacteria was significantly lower in samples from infants with botulism. Lactobacillus spp. abundance was notably reduced in 12 of the 14 samples. Clostridium botulinum and Clostridium baratii were identified in low relative abundances in confirmed and non-confirmed samples based on their 16S rRNA gene profiles, although their toxigenicity remained undetermined. No significant differences were observed in the number of operational taxonomic units (OTUs) observed or in fecal microbiota diversity between laboratory-confirmed and non-confirmed samples. Correlations between individual phylum abundances and infant age were variable, and no significant differences were shown in number of OTUs observed or in fecal microbiota diversity between samples delineated by overall mean age. CONCLUSIONS Significant differences in Proteobacteria, Firmicutes, and Enterobacteriaceae abundances were identified in the fecal microbiota of infants with botulism when compared to samples from non-confirmed cases. Fecal microbiota diversity was not significantly altered in infants with botulism, and a limited presence of BTPC was shown. It could not be determined whether the fecal microbiota profiles shown here were comparable prior to patient illness, or whether they were the direct result of infant botulism. The results of this study do, however, provide a detailed and descriptive observation into the infant gut microbiota after intestinal colonization by BTPC.
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Affiliation(s)
- T Brian Shirey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Janet K Dykes
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Carolina Lúquez
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Susan E Maslanka
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Brian H Raphael
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
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Amato KR, Yeoman CJ, Cerda G, Schmitt CA, Cramer JD, Miller MEB, Gomez A, Turner TR, Wilson BA, Stumpf RM, Nelson KE, White BA, Knight R, Leigh SR. Variable responses of human and non-human primate gut microbiomes to a Western diet. Microbiome 2015; 3:53. [PMID: 26568112 PMCID: PMC4645477 DOI: 10.1186/s40168-015-0120-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/29/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND The human gut microbiota interacts closely with human diet and physiology. To better understand the mechanisms behind this relationship, gut microbiome research relies on complementing human studies with manipulations of animal models, including non-human primates. However, due to unique aspects of human diet and physiology, it is likely that host-gut microbe interactions operate differently in humans and non-human primates. RESULTS Here, we show that the human microbiome reacts differently to a high-protein, high-fat Western diet than that of a model primate, the African green monkey, or vervet (Chlorocebus aethiops sabaeus). Specifically, humans exhibit increased relative abundance of Firmicutes and reduced relative abundance of Prevotella on a Western diet while vervets show the opposite pattern. Predictive metagenomics demonstrate an increased relative abundance of genes associated with carbohydrate metabolism in the microbiome of only humans consuming a Western diet. CONCLUSIONS These results suggest that the human gut microbiota has unique properties that are a result of changes in human diet and physiology across evolution or that may have contributed to the evolution of human physiology. Therefore, the role of animal models for understanding the relationship between the human gut microbiota and host metabolism must be re-focused.
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Affiliation(s)
- Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, USA.
- Department of Anthropology, University of Colorado Boulder, Boulder, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, USA.
| | - Carl J Yeoman
- Department of Range Sciences, Montana State University, Bozeman, USA.
| | - Gabriela Cerda
- Department of Anthropology, University of Illinois, Urbana, USA.
| | - Christopher A Schmitt
- Department of Anthropology, Boston University, Boston, USA.
- Center for Neurobehavioral Genetics, University of California, Los Angeles, CA, USA.
| | - Jennifer Danzy Cramer
- Department of Sociology, Anthropology, and Women's Studies, American Military University and American Public University, Charles Town, USA.
| | | | - Andres Gomez
- The Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, USA.
| | - Trudy R Turner
- Department of Anthropology, University of Wisconsin, Milwaukee, USA.
- Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Brenda A Wilson
- The Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
- Department of Microbiology, University of Illinois, Urbana, USA.
| | - Rebecca M Stumpf
- Department of Anthropology, University of Illinois, Urbana, USA.
- The Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
| | | | - Bryan A White
- The Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
- Department of Animal Sciences, University of Illinois, Urbana, USA.
| | - Rob Knight
- School of Medicine, University of California San Diego, La Jolla, USA.
| | - Steven R Leigh
- Department of Anthropology, University of Colorado Boulder, Boulder, USA.
- The Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
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Gam ZBA, Daumas S, Casalot L, Bartoli-Joseph M, Necib S, Linard Y, Labat M. Thermanaeromonas burensis sp. nov., a thermophilic anaerobe isolated from a subterranean clay environment. Int J Syst Evol Microbiol 2015; 66:445-449. [PMID: 26541283 DOI: 10.1099/ijsem.0.000739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, thermophilic and halotolerant strain, designated IA106T, was isolated from the seepage water collected in a metal biocorrosion test at a depth of 490 m, in a 130-160 m thick, subterranean Callovo-Oxfordian clay formation (158-152 million years old) in northern France. This geological formation has been selected as the potential host rock for the French high-level nuclear waste repository. Cells of strain IA106T stained Gram-positive and were non-motile, spore-forming, straight rods (0.5 × 2-6 μm). The five major fatty acids were C16 : 0 (15.9 %), C18 : 0 (15.4 %), iso-C17 : 1 I and/or anteiso-C17 : 1 B(14.8 %), iso-C17 : 0 (14.7 %) and iso-C15 : 0 (13.0 %). Growth was observed at temperatures ranging from 55 to 70 °C and at pH 5.5-9. The salinity range for growth was 0-20 g NaCl 1- 1. Yeast extract was required for growth. Strain IA106T was able to grow on lactate and various sugars in the presence of thiosulfate as electron acceptor. Sulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 60.2 mol%. 16S rRNA gene sequence analysis indicated that strain IA106T belonged to the family Thermoanaerobacteraceae, class Clostridia, phylum Firmicutes, and was most closely related to Thermanaeromonas toyohensis DSM 14490T (95.16 % 16S rRNA gene sequence similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain IA106T represents a novel species of the genus Thermanaeromonas, for which the name Thermanaeromonas burensis sp. nov. is proposed. The type strain is IA106T ( = DSM 26576T = JCM 18718T).
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Affiliation(s)
- Zouhaier Ben Ali Gam
- Laboratoire de Microbiologie IRD, Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MI0 UM110, 163 avenue de Luminy, case 925, F-13288 Marseille cedex 9, France
| | - Sylvie Daumas
- CFG Services groupe BRGM, 117 avenue de Luminy, 13009 Marseille, France
| | - Laurence Casalot
- Laboratoire de Microbiologie IRD, Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MI0 UM110, 163 avenue de Luminy, case 925, F-13288 Marseille cedex 9, France
| | - Manon Bartoli-Joseph
- Laboratoire de Microbiologie IRD, Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MI0 UM110, 163 avenue de Luminy, case 925, F-13288 Marseille cedex 9, France
| | - Sophia Necib
- Agence nationale pour la gestion des déchets radioactifs (Andra), Centre de Meuse/Haute-Marne, F-55290 Bure, France
| | - Yannick Linard
- Agence nationale pour la gestion des déchets radioactifs (Andra), Centre de Meuse/Haute-Marne, F-55290 Bure, France
| | - Marc Labat
- Laboratoire de Microbiologie IRD, Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MI0 UM110, 163 avenue de Luminy, case 925, F-13288 Marseille cedex 9, France
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Liu X, Cheng X, Wang H, Wang K, Qiao K. Effect of fumigation with 1,3-dichloropropene on soil bacterial communities. Chemosphere 2015; 139:379-385. [PMID: 26210186 DOI: 10.1016/j.chemosphere.2015.07.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
1,3-Dichloropropene (1,3-D) is a potential candidate as a soil fumigant because of the restriction of methyl bromide (MB) in soil fumigation. So far, little is known about the bacteria diversity in 1,3-D fumigated soil. Therefore, the impact of 1,3-D on soil bacterial community was determined by the 16S rRNA gene amplicon 454 sequencing. A total of 230,617 valid reads and 19,366 OTUs were obtained from the thirteen samples. 454 sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Firmicutes were predominant phylum in soils. Bacterial diversity was affected initially, while recovered in the later treatments and soils from 1,3-D treatment plots had a higher bacterial diversity. The results of this study demonstrated that 1,3-D had only a short-term and transitory impact on the indigenous soil microbial community. Our study would provide useful information for evaluating ecological safety of 1,3-D in China.
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Affiliation(s)
- Xiumei Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Xingkai Cheng
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Hongyan Wang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, People's Republic of China.
| | - Kaiyun Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Kang Qiao
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
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232
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Jones RT, Borchert J, Eisen R, MacMillan K, Boegler K, Gage KL. Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda. PLoS One 2015; 10:e0141057. [PMID: 26485147 PMCID: PMC4617453 DOI: 10.1371/journal.pone.0141057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/01/2015] [Indexed: 11/19/2022] Open
Abstract
The vast majority of human plague cases currently occur in sub-Saharan Africa. The primary route of transmission of Yersinia pestis, the causative agent of plague, is via flea bites. Non-pathogenic flea-associated bacteria may interact with Y. pestis within fleas and it is important to understand what factors govern flea-associated bacterial assemblages. Six species of fleas were collected from nine rodent species from ten Ugandan villages between October 2010 and March 2011. A total of 660,345 16S rRNA gene DNA sequences were used to characterize bacterial communities of 332 individual fleas. The DNA sequences were binned into 421 Operational Taxonomic Units (OTUs) based on 97% sequence similarity. We used beta diversity metrics to assess the effects of flea species, flea sex, rodent host species, site (i.e. village), collection date, elevation, mean annual precipitation, average monthly precipitation, and average monthly temperature on bacterial community structure. Flea species had the greatest effect on bacterial community structure with each flea species harboring unique bacterial lineages. The site (i.e. village), rodent host, flea sex, elevation, precipitation, and temperature also significantly affected bacterial community composition. Some bacterial lineages were widespread among flea species (e.g. Bartonella spp. and Wolbachia spp.), but each flea species also harbored unique bacterial lineages. Some of these lineages are not closely related to known bacterial diversity and likely represent newly discovered lineages of insect symbionts. Our finding that flea species has the greatest effect on bacterial community composition may help future investigations between Yersinia pestis and non-pathogenic flea-associated bacteria. Characterizing bacterial communities of fleas during a plague epizootic event in the future would be helpful.
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Affiliation(s)
- Ryan Thomas Jones
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
- Montana Institute on Ecosystems, Montana State University, Bozeman, Montana, United States of America
- * E-mail:
| | - Jeff Borchert
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Rebecca Eisen
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Katherine MacMillan
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Karen Boegler
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Kenneth L. Gage
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
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Abstract
This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 Pa). In assays with cell-free extract of cells grown with CO and fumarate, production of hydrogen from CO was not observed, and hydrogenase activity with benzyl viologen as electron acceptor was very low. Taken together, this suggested that CO is not utilized via hydrogen as intermediate. In the presence of CO, reduction of NADP+ was observed at a rate comparable to CO oxidation coupled to fumarate reduction in vivo. The G. sulfurreducens genome contains a single putative carbon monoxide dehydrogenase-encoding gene. The gene is part of a predicted operon also comprising a putative Fe–S cluster-binding subunit (CooF) and a FAD–NAD(P) oxidoreductase and is preceded by a putative CO-sensing transcription factor. This cluster may be involved in a novel pathway for CO oxidation, but further studies are necessary to ascertain this. Similar gene clusters are present in several other species belonging to the Deltaproteobacteria and Firmicutes, for which CO utilization is currently not known.
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Affiliation(s)
- Jeanine S Geelhoed
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
- NIOZ Royal Netherlands Institute for Sea Research, Korringaweg 7, 4401 NT, Yerseke, The Netherlands.
| | - Anne M Henstra
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Centre for Biomolecular Sciences, University of Nottingham, University Park, NG7 2EF, Nottingham, UK
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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234
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Liu TW, Park YM, Holscher HD, Padilla J, Scroggins RJ, Welly R, Britton SL, Koch LG, Vieira-Potter VJ, Swanson KS. Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity. PLoS One 2015; 10:e0136150. [PMID: 26301712 PMCID: PMC4547806 DOI: 10.1371/journal.pone.0136150] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
The gut microbiota is considered a relevant factor in obesity and associated metabolic diseases, for which postmenopausal women are particularly at risk. Increasing physical activity has been recognized as an efficacious approach to prevent or treat obesity, yet the impact of physical activity on the microbiota remains under-investigated. We examined the impacts of voluntary exercise on host metabolism and gut microbiota in ovariectomized (OVX) high capacity (HCR) and low capacity running (LCR) rats. HCR and LCR rats (age = 27wk) were OVX and fed a high-fat diet (45% kcal fat) ad libitum and housed in cages equipped with (exercise, EX) or without (sedentary, SED) running wheels for 11wk (n = 7-8/group). We hypothesized that increased physical activity would hinder weight gain, increase metabolic health and shift the microbiota of LCR rats, resulting in populations more similar to that of HCR rats. Animals were compared for characteristic metabolic parameters including body composition, lipid profile and energy expenditure; whereas cecal digesta were collected for DNA extraction. 16S rRNA gene-based amplicon Illumina MiSeq sequencing was performed, followed by analysis using QIIME 1.8.0 to assess cecal microbiota. Voluntary exercise decreased body and fat mass, and normalized fasting NEFA concentrations of LCR rats, despite only running one-third the distance of HCR rats. Exercise, however, increased food intake, weight gain and fat mass of HCR rats. Exercise clustered the gut microbial community of LCR rats, which separated them from the other groups. Assessments of specific taxa revealed significant (p<0.05) line by exercise interactions including shifts in the abundances of Firmicutes, Proteobacteria, and Cyanobacteria. Relative abundance of Christensenellaceae family was higher (p = 0.026) in HCR than LCR rats, and positively correlated (p<0.05) with food intake, body weight and running distance. These findings demonstrate that exercise differentially impacts host metabolism and gut microbial communities of female HCR and LCR rats without ovarian function.
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Affiliation(s)
- Tzu-Wen Liu
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Young-Min Park
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States of America
| | - Hannah D. Holscher
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States of America
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Child Health, University of Missouri, Columbia, Missouri, United States of America
| | - Rebecca J. Scroggins
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States of America
| | - Rebecca Welly
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States of America
| | - Steven L. Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lauren G. Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Victoria J. Vieira-Potter
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States of America
| | - Kelly S. Swanson
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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235
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Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y, Takase K. Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing. BMC Gastroenterol 2015; 15:100. [PMID: 26261039 PMCID: PMC4531509 DOI: 10.1186/s12876-015-0330-2] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/30/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Obesity has become one of the most serious social problems in developed countries, including Japan. The relationship between the gut microbiota and obesity has recently attracted the attention of many researchers. Although the gut microbiota was long thought to contribute to obesity, the exact association remains largely unknown. We examined the human gut microbiota composition in a Japanese population in order to determine its relationship to obesity. METHODS Stool samples from 23 non-obese subjects (body mass index [BMI] <20 kg/m(2)) and 33 obese subjects (BMI ≥25 kg/m(2)) were collected and DNA was extracted prior to colonoscopy. After terminal restriction fragment length polymorphism (T-RFLP) analysis, samples from 10 subjects (4 non-obese and 6 obese) were selected and subjected to next-generation sequencing for species-level analysis. RESULTS T-RFLP analysis showed significantly reduced numbers of Bacteroidetes and a higher Firmicutes to Bacteroidetes ratio in obese subjects compared with non-obese subjects. Bacterial diversity was significantly greater in obese subjects compared with non-obese subjects. Next-generation sequencing revealed that obese and non-obese subjects had different gut microbiota compositions and that certain bacterial species were significantly associated with each group (obese: Blautia hydrogenotorophica, Coprococcus catus, Eubacterium ventriosum, Ruminococcus bromii, Ruminococcus obeum; non-obese: Bacteroides faecichinchillae, Bacteroides thetaiotaomicron, Blautia wexlerae, Clostridium bolteae, Flavonifractor plautii). CONCLUSION Gut microbial properties differ between obese and non-obese subjects in Japan, suggesting that gut microbiota composition is related to obesity.
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Affiliation(s)
- Chika Kasai
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
| | - Kazushi Sugimoto
- Department of Molecular and Laboratory Medicine, Mie University School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan.
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Japan.
| | - Isao Moritani
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
| | - Junichiro Tanaka
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
| | - Yumi Oya
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
| | - Hidekazu Inoue
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
| | - Masahiko Tameda
- Department of Molecular and Laboratory Medicine, Mie University School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan.
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Japan.
| | - Katsuya Shiraki
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Japan.
| | - Masaaki Ito
- Department of Cardiology and Nephrology, Tsu, Japan.
| | - Yoshiyuki Takei
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Japan.
| | - Kojiro Takase
- Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan.
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Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol 2015; 21:8787-8803. [PMID: 26269668 PMCID: PMC4528021 DOI: 10.3748/wjg.v21.i29.8787] [Citation(s) in RCA: 1425] [Impact Index Per Article: 158.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 05/10/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023] Open
Abstract
Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual’s life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool.
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Glassner H, Zchori-Fein E, Compant S, Sessitsch A, Katzir N, Portnoy V, Yaron S. Characterization of endophytic bacteria from cucurbit fruits with potential benefits to agriculture in melons (Cucumis melo L.). FEMS Microbiol Ecol 2015; 91:fiv074. [PMID: 26183916 DOI: 10.1093/femsec/fiv074] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 11/14/2022] Open
Abstract
Endophytes are microorganisms that mainly colonize vegetative parts, but are also found in reproductive and disseminating organs, and may have beneficial characteristics. To identify microorganisms associated with the agriculturally important family, Cucurbitaceae, endophytes were initially determined in fruits of Cucumis melo Reticulatus Group 'Dulce' by a cultivation-independent approach based on fluorescence in situ hybridization using double labeling of oligonucleotide probes. Alpha-, Beta-, Gammaproteobacteria, Firmicutes and Actinobacteria were localized inside the fruits. Culturable bacteria were further isolated and identified from fruit tissues of 'Dulce', from fruits of other cultivated and wild-field-grown Cucurbitaceae, and from wild fruits growing under natural conditions. Low densities of culturable bacteria were detected in the investigated fruits, especially in four out of the five wild species, regardless of their growing environment. Substantial differences were observed between the wild and cultivated cucurbit taxa in regard to the number of colonized fruits as well as the type of endophytes. Bacillus was the most dominant genus of endophytes colonizing fruits of Cucurbitaceae. The antagonistic effects of isolated endophytes were assessed against cucurbit disease agents in dual-culture assays. Several bacterial isolates exhibited antagonistic properties against the tested plant pathogens. The identified bacteria may be useful for protecting plants not only in the field, but also for post-harvest.
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Affiliation(s)
- Hanoch Glassner
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel ARO, Dept. of Entomology, Newe Ya'ar Research Center 30095, Israel
| | | | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Nurit Katzir
- ARO, Agricultural Research Organization, Dept. of Vegetable Crops, Newe Ya'ar Research Center 30095, Israel
| | - Vitaly Portnoy
- ARO, Agricultural Research Organization, Dept. of Vegetable Crops, Newe Ya'ar Research Center 30095, Israel
| | - Sima Yaron
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
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Oh C, Lee K, Cheong Y, Lee SW, Park SY, Song CS, Choi IS, Lee JB. Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing. PLoS One 2015; 10:e0131468. [PMID: 26134411 PMCID: PMC4489859 DOI: 10.1371/journal.pone.0131468] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/02/2015] [Indexed: 11/21/2022] Open
Abstract
The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%), Proteobacteria (21.6%), Bacteroidetes (9.8%), Actinobacteria (7.1%), and Fusobacteria (3.9%) were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%), Actinobacteria (21%), Bacteroidetes (19.7%), Firmicutes (19.3%), and Fusobacteria (12.3%) were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%), Neisseria (10.3%), Haemophilus (9.6%), Prevotella (8.4%), and Veillonella (8.1%), whereas the predominant genera in the canine samples were Actinomyces (17.2%), Unknown (16.8), Porphyromonas (14.8), Fusobacterium (11.8), and Neisseria (7.2%). The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.
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Affiliation(s)
- Changin Oh
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Kunkyu Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Yeotaek Cheong
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Sang-Won Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Seung-Yong Park
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Chang-Seon Song
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - In-Soo Choi
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Joong-Bok Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
- * E-mail:
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Ritchie LE, Taddeo SS, Weeks BR, Lima F, Bloomfield SA, Azcarate-Peril MA, Zwart SR, Smith SM, Turner ND. Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis. PLoS One 2015; 10:e0125792. [PMID: 26083373 PMCID: PMC4470690 DOI: 10.1371/journal.pone.0125792] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/26/2015] [Indexed: 01/01/2023] Open
Abstract
Astronaut intestinal health may be impacted by microgravity, radiation, and diet. The aim of this study was to characterize how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted to achieve these goals: 1) fractionated low LET γ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET γ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. Low LET radiation, IRON and spaceflight increased Bacteroidetes and decreased Firmicutes. RAD and IRON+RAD increased Lactobacillales and lowered Clostridiales compared to the control (CON) and IRON treatments. Low LET radiation, IRON, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Although we noted no differences in colon epithelial injury or inflammation, spaceflight elevated TGFβ gene expression. Microbiota and mucosal characterization in these models is a first step in understanding the impact of the space environment on intestinal health.
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Affiliation(s)
- Lauren E. Ritchie
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, Texas, United States of America
| | - Stella S. Taddeo
- Nutrition & Food Science Department, Texas A&M University, College Station, Texas, United States of America
| | - Brad R. Weeks
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Florence Lima
- Division of Nephrology, Department of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Susan A. Bloomfield
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, United States of America
| | - M. Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Sara R. Zwart
- Human Health and Performance Directorate, NASA Lyndon B. Johnson Space Center, Houston, Texas, United States of America
| | - Scott M. Smith
- Human Health and Performance Directorate, NASA Lyndon B. Johnson Space Center, Houston, Texas, United States of America
| | - Nancy D. Turner
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, Texas, United States of America
- Nutrition & Food Science Department, Texas A&M University, College Station, Texas, United States of America
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240
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Ammons MCB, Morrissey K, Tripet BP, Van Leuven JT, Han A, Lazarus GS, Zenilman JM, Stewart PS, James GA, Copié V. Biochemical association of metabolic profile and microbiome in chronic pressure ulcer wounds. PLoS One 2015; 10:e0126735. [PMID: 25978400 PMCID: PMC4433261 DOI: 10.1371/journal.pone.0126735] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/26/2022] Open
Abstract
Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the biochemical associations between the taxonomic and metabolomic profiles of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Biochemical association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.
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Affiliation(s)
- Mary Cloud B. Ammons
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (VC); (MCBA)
| | - Kathryn Morrissey
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Brian P. Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - James T. Van Leuven
- Division of Biological Science, University of Montana, Missoula, Montana, United States of America
| | - Anne Han
- Department of Dermatology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Gerald S. Lazarus
- Department of Dermatology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Jonathan M. Zenilman
- Department of Dermatology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Philip S. Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Garth A. James
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (VC); (MCBA)
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241
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Frykman PK, Nordenskjöld A, Kawaguchi A, Hui TT, Granström AL, Cheng Z, Tang J, Underhill DM, Iliev I, Funari VA, Wester T. Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study. PLoS One 2015; 10:e0124172. [PMID: 25909773 PMCID: PMC4409062 DOI: 10.1371/journal.pone.0124172] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/10/2015] [Indexed: 01/01/2023] Open
Abstract
Development of potentially life-threatening enterocolitis is the most frequent complication in children with Hirschsprung disease (HSCR), even after definitive corrective surgery. Intestinal microbiota likely contribute to the etiology of enterocolitis, so the aim of this study was to compare the fecal bacterial and fungal communities of children who developed Hirschsprung-associated enterocolitis (HAEC) with HSCR patients who had never had enterocolitis. Eighteen Hirschsprung patients who had completed definitive surgery were enrolled: 9 had a history of HAEC and 9 did not. Fecal DNA was isolated and 16S and ITS-1 regions sequenced using Next Generation Sequencing and data analysis for species identification. The HAEC group bacterial composition showed a modest reduction in Firmicutes and Verrucomicrobia with increased Bacteroidetes and Proteobacteria compared with the HSCR group. In contrast, the fecal fungi composition of the HAEC group showed marked reduction in diversity with increased Candida sp., and reduced Malassezia and Saccharomyces sp. compared with the HSCR group. The most striking finding within the HAEC group is that the Candida genus segregated into “high burden” patients with 97.8% C. albicans and 2.2% C. tropicalis compared with “low burden” patients 26.8% C. albicans and 73% C. tropicalis. Interestingly even the low burden HAEC group had altered Candida community structure with just two species compared to more diverse Candida populations in the HSCR patients. This is the first study to identify Candida sp. as potentially playing a role in HAEC either as expanded commensal species as a consequence of enterocolitis (or treatment), or possibly as pathobioants contributing to the pathogenesis of HAEC. These findings suggest a dysbiosis in the gut microbial ecosystem of HAEC patients, such that there may be dominance of fungi and bacteria predisposing patients to development of HAEC.
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Affiliation(s)
- Philip K. Frykman
- Division of Pediatric Surgery, Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- * E-mail:
| | - Agneta Nordenskjöld
- Department of Pediatric Surgery, Astrid Lindgren’s Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Akemi Kawaguchi
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Thomas T. Hui
- Division of Pediatric Surgery, Children’s Hospital Oakland, Oakland, California, United States of America
| | - Anna L. Granström
- Department of Pediatric Surgery, Astrid Lindgren’s Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Zhi Cheng
- Division of Pediatric Surgery, Departments of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jie Tang
- Genomics Core Laboratory, Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David M. Underhill
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Iliyan Iliev
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Vince A. Funari
- Genomics Core Laboratory, Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Tomas Wester
- Department of Pediatric Surgery, Astrid Lindgren’s Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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242
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Falcone-Dias MF, Centrón D, Pavan F, Moura ACDS, Naveca FG, de Souza VC, Farache Filho A, Leite CQF. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance. PLoS One 2015; 10:e0121284. [PMID: 25803794 PMCID: PMC4372423 DOI: 10.1371/journal.pone.0121284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/29/2015] [Indexed: 11/24/2022] Open
Abstract
Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.
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Affiliation(s)
- Maria Fernanda Falcone-Dias
- School of Pharmaceutical Sciences, UNESP- Univ Estadual Paulista, Araraquara, SP, Brazil
- Departamento de Microbiología, Facultad de Medicina, UBA, Buenos Aires, Argentina
- * E-mail:
| | - Daniela Centrón
- Departamento de Microbiología, Facultad de Medicina, UBA, Buenos Aires, Argentina
| | - Fernando Pavan
- School of Pharmaceutical Sciences, UNESP- Univ Estadual Paulista, Araraquara, SP, Brazil
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243
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Zhao W, Wang Y, Liu S, Huang J, Zhai Z, He C, Ding J, Wang J, Wang H, Fan W, Zhao J, Meng H. The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments. PLoS One 2015; 10:e0117441. [PMID: 25688558 PMCID: PMC4331431 DOI: 10.1371/journal.pone.0117441] [Citation(s) in RCA: 240] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 12/23/2014] [Indexed: 12/24/2022] Open
Abstract
Metagenome of gut microbes has been implicated in metabolism, immunity, and health maintenance of its host. However, in most of previous studies, the microbiota was sampled from feces instead of gastrointestinal (GI) tract. In this study, we compared the microbial populations from feces at four different developmental stages and contents of four intestinal segments at maturity to examine the dynamic shift of microbiota in pigs and investigated whether adult porcine fecal samples could be used to represent samples of the GI tract. Analysis results revealed that the ratio of Firmicutes to Bacteroidetes from the feces of the older pigs (2-, 3-, 6- month) were 10 times higher compared to those from piglets (1-month). As the pigs matured, so did it seem that the composition of microbiome became more stable in feces. In adult pigs, there were significant differences in microbial profiles between the contents of the small intestine and large intestine. The dominant genera in the small intestine belonged to aerobe or facultative anaerobe categories, whereas the main genera in the large intestine were all anaerobes. Compared to the GI tract, the composition of microbiome was quite different in feces. The microbial profile in large intestine was more similar to feces than those in the small intestine, with the similarity of 0.75 and 0.38 on average, respectively. Microbial functions, predicted by metagenome profiles, showed the enrichment associated with metabolism pathway and metabolic disease in large intestine and feces while higher abundance of infectious disease, immune function disease, and cancer in small intestine. Fecal microbes also showed enriched function in metabolic pathways compared to microbes from pooled gut contents. Our study extended the understanding of dynamic shift of gut microbes during pig growth and also characterized the profiles of bacterial communities across GI tracts of mature pigs.
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Affiliation(s)
- Wenjing Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
| | - Yapeng Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P. R. China
| | - Shuyun Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
| | - Jiaojiao Huang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P. R. China
| | - Zhengxiao Zhai
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
| | - Chuan He
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
- Shanghai Personal Biotechnology Limited Company, Shanghai, P. R. China
| | - Jinmei Ding
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
| | - Jun Wang
- Shanghai Personal Biotechnology Limited Company, Shanghai, P. R. China
| | - Huijuan Wang
- Shanghai Personal Biotechnology Limited Company, Shanghai, P. R. China
| | - Weibing Fan
- Shanghai Personal Biotechnology Limited Company, Shanghai, P. R. China
| | - Jianguo Zhao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P. R. China
- * E-mail: (JZ); (HM)
| | - He Meng
- School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, P. R. China
- * E-mail: (JZ); (HM)
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244
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Pitta DW, Parmar N, Patel AK, Indugu N, Kumar S, Prajapathi KB, Patel AB, Reddy B, Joshi C. Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle. PLoS One 2014; 9:e111710. [PMID: 25365522 PMCID: PMC4218807 DOI: 10.1371/journal.pone.0111710] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022] Open
Abstract
The ruminal microbiome in herbivores plays a dominant role in the digestion of lignocellulose and has potential to improve animal productivity. Kankrej cattle, a popular native breed of the Indian subcontinent, were used to investigate the effect of different dietary treatments on the bacterial diversity in ruminal fractions using different primer pairs. Two groups of four cows were assigned to two primary diets of either dry or green forages. Each group was fed one of three dietary treatments for six weeks each. Dietary treatments were; K1 (50% dry/green roughage: 50% concentrate), K2 (75% dry/green roughage: 25% concentrate) and K3 (100% dry/green roughage). Rumen samples were collected using stomach tube at the end of each dietary period and separated into solid and liquid fractions. The DNA was extracted and amplified for V1–V3, V4–V5 and V6–V8 hypervariable regions using P1, P2 and P3 primer pairs, sequenced on a 454 Roche platform and analyzed using QIIME. Community compositions and the abundance of most bacterial lineages were driven by interactions between primer pair, dietary treatment and fraction. The most abundant bacterial phyla identified were Bacteroidetes and Firmicutes however, the abundance of these phyla varied between different primer pairs; in each primer pair the abundance was dependent on the dietary treatment and fraction. The abundance of Bacteroidetes in cattle receiving K1 treatment indicate their diverse functional capabilities in the digestion of both carbohydrate and protein while the predominance of Firmicutes in the K2 and K3 treatments signifies their metabolic role in fibre digestion. It is apparent that both liquid and solid fractions had distinct bacterial community patterns (P<0.001) congruent to changes in the dietary treatments. It can be concluded that the P1 primer pair flanking the V1–V3 hyper-variable region provided greater species richness and diversity of bacterial populations in the rumen of Kankrej cattle.
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Affiliation(s)
- Dipti W. Pitta
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Nidhi Parmar
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Amrut K. Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Nagaraju Indugu
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sanjay Kumar
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karsanbhai B. Prajapathi
- Livestock Production and Management Department, College of Veterinary Science and Animal Husbandry, Sardar Krushi Nagar Dantiwada Agricultural University, Sardar Krushi Nagar, Gujarat, India
| | - Anand B. Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Bhaskar Reddy
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya Joshi
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
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