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Cui W, Ma Z, Li X, Hu X. Structural rearrangement of native and processed pea starches following simulated digestion in vitro and fermentation characteristics of their resistant starch residues using human fecal inoculum. Int J Biol Macromol 2021; 172:490-502. [PMID: 33472022 DOI: 10.1016/j.ijbiomac.2021.01.092] [Citation(s) in RCA: 10] [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] [Received: 10/19/2020] [Revised: 12/27/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Pea starches, in both native (NPS) and retrograded-autoclaved forms (RAPS), were subjected to simulated gastrointestinal (GI) digestion in vitro, their multi-scale structural characteristics, morphological features, molecular distribution and thermal properties were characterized. A gradual increase in the short-/long-range crystallinity, melting enthalpy of gelatinization on increasing digestion time was observed for both the native and retrograded-autoclaved pea starch samples based on the X-ray diffraction, Fourier-transform infrared spectra, solid-state 13CNMR and differential scanning calorimetry measurements. It was especially noticed that the growth rate of crystallinity and double helices, as well as the decrease in Mw values were evidently greater for RAPS than for NPS. To investigate how different molecular fine structure of pea starch substrate affects the gut microbiota shifts and dynamic short-chain fatty acid profile, their resistant starch residues obtained from both native and retrograded-autoclaved pea starch after 8 h of simulated GI tract digestion was used as the fermentation substrate. The levels of acetate, propionate and butyrate gradually increased with the increasing fermentation time for NPS and RAPS. In comparison to the blank control (i.e., the group without the addition of carbohydrate), the fermented NPS and RAPS obviously resulted in an increased abundance of Firmicutes and Bacteroidetes, accompanied by a decrease in Proteobacteria, Actinobacteria and Verrucomicrobia. Both NPS and RAPS promoted different shifts in the microbial community at the genus level, with an increase in the abundance of Bacteroides, Megamonas and Bifidobacterium, as well as a reduction in the abundance of Fusobacterium, Faecalibacterium and Lachnoclostridium in comparison to the blank control samples.
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Affiliation(s)
- Wenxin Cui
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Zhen Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.
| | - Xiaoping Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
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Panchavinin S, Tobino T, Hara-Yamamura H, Matsuura N, Honda R. Candidates of quorum sensing bacteria in activated sludge associated with N-acyl homoserine lactones. Chemosphere 2019; 236:124292. [PMID: 31310968 DOI: 10.1016/j.chemosphere.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/28/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
This study aimed to explore candidates of microbial groups which is associated with quorum sensing in activated sludge. Activated sludge samples were collected from three wastewater treatment plants (WWTP) to analyze N-acyl homoserine lactone (AHL) by Fourier-transform mass spectrometry (FTMS) and 16S rRNA-based microbial community. Among activated sludge samples taken at 3 WWTPs in different seasons, 2 AHL species of N-3-hydroxyoctanoyl-l-homoserine lactone and N-3-hydroxydecanoyl-l-homoserine lactone were detected in the range of ranged of 0.1 ng/L to 1.6 ng/L. The detected AHL species were not dependent on treatment systems nor seasons. From microbial community analysis, population abundance of one strain in Verrucomicrobia and two strains in Holophagaceae had high correlation with AHL concentration in activated sludge. Comamonadaceae had also moderately correlated population with AHL concentrations among quorum sensing bacteria reported previously.
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Affiliation(s)
- Smarch Panchavinin
- Department of Environmental Design, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, 920-1192, Japan.
| | - Tomohiro Tobino
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Hiroe Hara-Yamamura
- Research Center for Sustainable Energy and Technology, Kanazawa University, Ishikawa, 920-1192, Japan.
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, 920-1192, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, 920-1192, Japan.
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Xing J, Li X, Sun Y, Zhao J, Miao S, Xiong Q, Zhang Y, Zhang G. Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species. Genes Genomics 2019; 41:1253-1264. [PMID: 31399846 PMCID: PMC6828834 DOI: 10.1007/s13258-019-00855-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 03/13/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022]
Abstract
Background Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. Objective In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. Methods Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. Results The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. Conclusion Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future. Electronic supplementary material The online version of this article (10.1007/s13258-019-00855-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juyuan Xing
- Wuhan University of Technology, Wuhan, Hubei People’s Republic of China
| | - Xiaobo Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Yingjiao Sun
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Juanjuan Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Shaohua Miao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Qin Xiong
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Yonggang Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), No. 19 Keyuan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Guishan Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081 People’s Republic of China
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Abstract
A Gram-stain negative, spherical, obligately aerobic bacterium, designated strain WN38T, was isolated from a marine solar saltern on the coast of Weihai, China. Optimal growth occurred at 33 °C, pH 7.0-7.5 and in the presence of 3-4 % (w/v) NaCl. The genome of strain WN38T was found to contain the genes necessary for arsenate reductase and related proteins, indicating that it may have potential in bioremediation of heavy metal polluted environments. Comparative 16S rRNA gene sequence analysis showed that strain WN38T represented a member of the genus Coraliomargarita, and was related most closely to Coraliomargarita akajimensis KCTC 12865T (95.7 %). Pairwise sequence similarities to all other type strains of species were below 90 %. Genome-based calculations (average nucleotide identity, genome-to-genome distance and DNA G+C percentage) and results of pairwise amino acid identity (AAI >60 %) and percentage of conserved proteins (POCP >50 %) also indicated clearly that strain WN38T represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the sole respiratory quinone was menaquinone-7 (MK-7) and a fatty acid profile with iso-C14 : 0, C18 : 0 and C18 : 1ω9c as major components, supported this finding at the same time as contributing to a comprehensive characterization of strain WN38T. On the basis of its phenotypic and genotypic properties, strain WN38T represents a novel species of the genus Coraliomargarita, for which the name Coraliomargaritasinensis sp. nov. is proposed. The type strain is WN38T (=KCTC 62602T=MCCC 1H00313T).
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Affiliation(s)
- Liu-Yan Zhou
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Nan-Nan Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Da-Shuai Mu
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Yan Liu
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A, Johengen TH, Palladino D, Denef VJ. Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One 2018; 13:e0195112. [PMID: 29590198 PMCID: PMC5874073 DOI: 10.1371/journal.pone.0195112] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 10/16/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7–41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.
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Affiliation(s)
- Edna Chiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Marian L. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Michelle A. Berry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, United States of America
| | - Ashley Burtner
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Danna Palladino
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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Suriano F, Bindels LB, Verspreet J, Courtin CM, Verbeke K, Cani PD, Neyrinck AM, Delzenne NM. Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity. Sci Rep 2017; 7:5621. [PMID: 28717237 PMCID: PMC5514075 DOI: 10.1038/s41598-017-05698-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 12/15/2016] [Accepted: 06/02/2017] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to determine the impact of different wheat bran fractions on the gut microbiota and fat binding capacity to explain their differential effects on metabolic and inflammatory disorders induced by a western diet (WD) in mice. Wheat bran derived arabinoxylan oligosaccharides (AXOS), a crude fraction of wheat bran (WB), or the same wheat bran with reduced particle size (WBs) were added to the WD of mice for 8 weeks. AXOS shifted the gut microbiota composition, blunted Clostridium and Turicibacter genera and strongly promoted Bifidobacterium and Butyricicoccus genera, independently of changes in gut antimicrobial peptide expression. AXOS was the most efficient to reduce adiposity. Only WB fraction promoted fat excretion and differed from the other fractions by the capacity to increase the Akkermansia genus and to counteract gut interleukin 1 beta (IL1β) overexpression. Strikingly, WBs promoted steatosis and adipose tissue inflammation, despite its ability -like WB- to increase bacterial diversity. In conclusion, wheat bran fractions differently affect metabolic and inflammatory disorders associated with WD feeding, depending on their particle size, their fat binding capacity and their influence on the gut microbiota. Those results might be useful to take into account in nutritional advices to control obesity.
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Affiliation(s)
- Francesco Suriano
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Joran Verspreet
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition, Research Center (LFoRCe). KU Leuven, B-3001, Leuven, Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition, Research Center (LFoRCe). KU Leuven, B-3001, Leuven, Belgium
| | - Kristin Verbeke
- Translational Research Center for Gastrointestinal Disorders and Leuven Food Science and Nutrition Center, KU Leuven, B-3000, Leuven, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), Louvain Drug Research Institute, UCL, B-1200, Brussels, Belgium
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium.
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Soto Del Rio MDLD, Dalmasso A, Civera T, Bottero MT. Characterization of bacterial communities of donkey milk by high-throughput sequencing. Int J Food Microbiol 2017; 251:67-72. [PMID: 28431310 DOI: 10.1016/j.ijfoodmicro.2017.03.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 10/28/2016] [Revised: 03/15/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The interest in donkey milk (DM) is growing because of its functional properties and nutritional value, especially for children with allergies and food intolerances. However, most of the available reports of DM microbiota are based on culture-dependent methods to investigate food safety issues and the presence of lactic acid bacteria (LAB). The aim of this study was to determine the composition of DM bacterial communities using a high-throughput sequencing (HTS) approach. Bulk milk samples from Italian donkey dairy farms from two consecutive years were analysed using the MiSeq Illumina platform. All sample reads were classified into five phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The most prevalent genera-Pseudomonas, Ralstonia, Acinetobacter, Cupriavidus, Citrobacter and Sphingobacterium-were Gram-negative bacteria. The core microbiota was composed of genera that comprise commonly associated milk bacteria, LAB and species normally found in soil, water and plants. Reads assigned to LAB genera-Streptococcus, Lactococcus, Enterococcus, Leuconostoc, Lactobacillus, and Carnobacterium-corresponded on average to 2.55% of the total reads per sample. Among these, the distribution of reads assigned to coccus- and bacillus-shaped LAB was variable between and within the farms, confirming their presence and suggesting a complex population of these bacteria in DM. The present study represents a general snapshot of the DM microbial population, underlining its variability and motivating further studies for the exploitation of the technological potential of bacteria naturally present in DM.
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Affiliation(s)
| | - Alessandra Dalmasso
- Dipartimento di Scienze Veterinarie, Università di Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
| | - Tiziana Civera
- Dipartimento di Scienze Veterinarie, Università di Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
| | - Maria Teresa Bottero
- Dipartimento di Scienze Veterinarie, Università di Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy.
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Wu X, Pedersen K, Edlund J, Eriksson L, Åström M, Andersson AF, Bertilsson S, Dopson M. Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters. Microbiome 2017; 5:37. [PMID: 28335808 PMCID: PMC5364579 DOI: 10.1186/s40168-017-0253-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 03/12/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. CONCLUSIONS Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.
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Affiliation(s)
- Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | | | | | | | - Mats Åström
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
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Torralba MG, Franks JS, Gomez A, Yooseph S, Nelson KE, Grimes DJ. Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico. Microb Ecol 2017; 73:91-100. [PMID: 27815589 DOI: 10.1007/s00248-016-0857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/03/2015] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
The environmental impact of major oil spills on marine microorganisms has yet to be thoroughly investigated using molecular biology techniques. The Deepwater Horizon (DWH) drilling rig explosion of 2010 affected an approximately 176,000 km2 surface area of the Gulf of Mexico (GOM) when an estimated 210 million gallons of oil from the Macondo Prospect spilled into the environment. Pelagic Sargassum, a complex of two surface drifting species (Sargassum natans and Sargassum fluitans) of marine brown macroalgae and a critically important habitat in the GOM ecosystem, was suffused by Macondo Prospect 252 oil released during the DWH event. Using 16S rRNA PCR and Roche 454 pyrosequencing, the effect of the oil on the bacterial population associated with pelagic Sargassum and contiguous waters was examined by comparing sequence data generated from samples collected from oiled and non-oiled locations in the northern GOM. Sequence data showed similar microbial composition in Sargassum regardless of exposure to oil primarily dominated by five phyla; Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and unclassified bacteria. The microbial composition in water samples was significantly less diverse than for Sargassum and consisted primarily of Proteobacteria, Firmicutes, and Bacteroidetes. Due to the evenly distributed abundance of microbial species on oiled and non-oiled pelagic Sargassum, study findings indicate that DWH spilled oil had minimal effect on the composition and diversity of the microbial community associated with Sargassum and contiguous waters. However, higher abundances of Sulfitobacter and one species of Psychrobacter were found in oiled water samples when compared to non-oiled water samples indicating some effect of DHW oil in the microbial composition of seawater. Though there are a number of marine studies using molecular biology approaches, this is the first molecular examination of the impact of the DWH oil spill on bacterial communities associated with pelagic Sargassum and contiguous waters from the GOM.
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Affiliation(s)
| | - James S Franks
- The University of Southern Mississippi, Gulf Coast Research Laboratory, Center for Fisheries Research and Development, 703 East Beach Drive, Ocean Springs, MS, 39564, USA
| | - Andres Gomez
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Shibu Yooseph
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - D Jay Grimes
- Division of Coastal Sciences, The University of Southern Mississippi, Gulf Coast Research Laboratory, 703 East Beach Drive, Ocean Springs, MS, 39564, USA.
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10
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de Almeida MLM, Feringer WH, Carvalho JRG, Rodrigues IM, Jordão LR, Fonseca MG, Carneiro de Rezende AS, de Queiroz Neto A, Weese JS, da Costa MC, Lemos EGDM, Ferraz GDC. Intense Exercise and Aerobic Conditioning Associated with Chromium or L-Carnitine Supplementation Modified the Fecal Microbiota of Fillies. PLoS One 2016; 11:e0167108. [PMID: 27935992 PMCID: PMC5147854 DOI: 10.1371/journal.pone.0167108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 07/07/2016] [Accepted: 11/07/2016] [Indexed: 12/27/2022] Open
Abstract
Recent studies performed in humans and rats have reported that exercise can alter the intestinal microbiota. Athletic horses perform intense exercise regularly, but studies characterizing horse microbiome during aerobic conditioning programs are still limited. Evidence has indicated that this microbial community is involved in the metabolic homeostasis of the host. Research on ergogenic substances using new sequencing technologies have been limited to the intestinal microbiota and there is a considerable demand for scientific studies that verify the effectiveness of these supplements in horses. L-carnitine and chromium are potentially ergogenic substances for athletic humans and horses since they are possibly able to modify the metabolism of carbohydrates and lipids. This study aimed to assess the impact of acute exercise and aerobic conditioning, associated either with L-carnitine or chromium supplementation, on the intestinal microbiota of fillies. Twelve “Mangalarga Marchador” fillies in the incipient fitness stage were distributed into four groups: control (no exercise), exercise, L-carnitine (10g/day) and chelated chromium (10mg/day). In order to investigate the impact of acute exercise or aerobic conditioning on fecal microbiota all fillies undergoing the conditioning program were analyzed as a separate treatment. The fillies underwent two incremental exercise tests before and after training on a treadmill for 42 days at 70–80% of the lactate threshold intensity. Fecal samples were obtained before and 48 h after acute exercise (incremental exercise test). Bacterial populations were characterized by sequencing the V4 region of the 16S rRNA gene using the MiSeq Illumina platform, and 5,224,389 sequences were obtained from 48 samples. The results showed that, overall, the two most abundant phyla were Firmicutes (50.22%) followed by Verrucomicrobia (15.13%). The taxa with the highest relative abundances were unclassified Clostridiales (17.06%) and "5 genus incertae sedis" from the phylum Verrucomicrobia (12.98%). There was a decrease in the phylum Chlamydiae and in the genus Mycobacterium after the second incremental exercise test. Intense exercise changed the community’s structure and aerobic conditioning was associated with changes in the composition and structure of the intestinal bacterial population of fillies. The intra-group comparison showed that chromium or L-carnitine induced moderate changes in the fecal microbiota of fillies, but the microbiota did not differ from the control group, which was exercised with no supplementation. Fecal pH correlated positively with Simpson’s index, while plasma pH correlated negatively. Our results show that exercise and aerobic conditioning can change in the microbiota and provide a basis for further studies enrolling a larger number of horses at different fitness levels to better understand the effects of exercise and training on the intestinal microbiota of horses.
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Affiliation(s)
- Maria Luiza Mendes de Almeida
- Department of Technology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Bioquímica de Microrganismos e Plantas, Jaboticabal, São Paulo, Brazil
| | - Walter Heinz Feringer
- Department of Animal Morphology and Physiology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Farmacologia e Fisiologia do Exercício Equino (LAFEQ), Jaboticabal, São Paulo, Brazil
| | - Júlia Ribeiro Garcia Carvalho
- Department of Animal Morphology and Physiology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Farmacologia e Fisiologia do Exercício Equino (LAFEQ), Jaboticabal, São Paulo, Brazil
| | - Isadora Mestriner Rodrigues
- Department of Animal Morphology and Physiology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Farmacologia e Fisiologia do Exercício Equino (LAFEQ), Jaboticabal, São Paulo, Brazil
| | - Lilian Rezende Jordão
- Department of Animal Sciences, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mayara Gonçalves Fonseca
- Department of Animal Sciences, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Antonio de Queiroz Neto
- Department of Animal Morphology and Physiology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Farmacologia e Fisiologia do Exercício Equino (LAFEQ), Jaboticabal, São Paulo, Brazil
| | - J. Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | | | - Eliana Gertrudes de Macedo Lemos
- Department of Technology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Bioquímica de Microrganismos e Plantas, Jaboticabal, São Paulo, Brazil
| | - Guilherme de Camargo Ferraz
- Department of Animal Morphology and Physiology, Faculdades de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista, Laboratório de Farmacologia e Fisiologia do Exercício Equino (LAFEQ), Jaboticabal, São Paulo, Brazil
- * E-mail:
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Danilova OV, Belova SE, Gagarinova IV, Dedysh SN. Microbial Community Composition and Methanotroph Diversity of a Subarctic Wetland in Russia. Mikrobiologiia 2016; 85:545-554. [PMID: 29364602] [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
This study assessed the microbial diversity, activity, and composition of methane-oxidizing communities of a subarctic wetland in Russia,with mosaic cover of Sphagnum mosses and lichens of the genera Cladonia and Cetraria. Potential methane-oxidizing activity of peat sampled from lichen-dominated wetland sites was higher than that in the sites dominated by Sphagnum mosses. In peat from lichendominated sites, major bacterial groups identified by high-throughput sequencing of the 16S rRNA genes were the Acidobacteria (35.4-41.2% of total 16S rRNA gene reads), Alphaproteobacteria (19.1-24.2%), Gammaproteobacteria (7.9-11.1%), Actinobacteria (5.5-13.2%), Planctomycetes (7.2-9.5%), and Verrucomicrobia (5.1-9.5%). The distinctive feature of this community was high proportion of Subdivision 2 Acidobacteria, which are not char- acteristic for boreal Sphagnum peat bogs. Methanotrophic community composition was determined by mo- lecular analysis of the pmoA gene encoding particulate methane monooxygenase. Most (-80%) of all pmoA gene fragments revealed in peat from lichen-dominated sites belonged to the phylogenetic lineage represented by a microaerobic spiral-shaped methanotroph, "Candidatus Methylospira mobilis." Members of the genus Methylocystis, which are typical inhabitants of boreal Sphagnum peat bogs, represented only a minor group of indigenous methanotrophs. The specific feature of a methanotrophic community in peat from lichen-dominated sites was the presence of uncultivated USCa (Upland Soil Cluster alpha) methanotrophs, which are typical for acidic upland soils showing atmospheric methane oxidation. The methanotrophic community composition in lichen-dominated sites of a tundra wetland, therefore, was markedly different from that in bo- real Sphagnum peat bogs.
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Chernitsyna SM, Khal'zov IA, Khanaeva TA, Morozov IV, Klimenkov IV, Pimenov NV, Zemskayal TI. Microbial Community Associated with Thioploca sp. Sheaths in the Area of the Posolski Bank Methane Seep, Southern Baikal. Mikrobiologiia 2016; 85:522-530. [PMID: 29364600] [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
Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolski Bank cold methane seep (southern Baikal) were -studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica.- Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as in- side and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells-without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic; of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were idenified in the sheath community: Bacteroidetes, Nitro- spira, Chloroflexi, Planctomycetes, Verrucomicrobia,'y-, and 6-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.
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Shono Y, Docampo MD, Peled JU, Perobelli SM, Velardi E, Tsai JJ, Slingerland AE, Smith OM, Young LF, Gupta J, Lieberman SR, Jay HV, Ahr KF, Rodriguez KAP, Xu K, Calarfiore M, Poeck H, Caballero S, Devlin SM, Rapaport F, Dudakov JA, Hanash AM, Gyurkocza B, Murphy GF, Gomes C, Liu C, Moss EL, Falconer SB, Bhatt AS, Taur Y, Pamer EG, van den Brink MR, Jenq RR. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med 2016; 8:339ra71. [PMID: 27194729 PMCID: PMC4991773 DOI: 10.1126/scitranslmed.aaf2311] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022]
Abstract
Intestinal bacteria may modulate the risk of infection and graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients often develop neutropenic fever, which is treated with antibiotics that may target anaerobic bacteria in the gut. We retrospectively examined 857 allo-HSCT recipients and found that treatment of neutropenic fever with imipenem-cilastatin and piperacillin-tazobactam antibiotics was associated with increased GVHD-related mortality at 5 years (21.5% for imipenem-cilastatin-treated patients versus 13.1% for untreated patients, P = 0.025; 19.8% for piperacillin-tazobactam-treated patients versus 11.9% for untreated patients, P = 0.007). However, two other antibiotics also used to treat neutropenic fever, aztreonam and cefepime, were not associated with GVHD-related mortality (P = 0.78 and P = 0.98, respectively). Analysis of stool specimens from allo-HSCT recipients showed that piperacillin-tazobactam administration was associated with perturbation of gut microbial composition. Studies in mice demonstrated aggravated GVHD mortality with imipenem-cilastatin or piperacillin-tazobactam compared to aztreonam (P < 0.01 and P < 0.05, respectively). We found pathological evidence for increased GVHD in the colon of imipenem-cilastatin-treated mice (P < 0.05), but no difference in the concentration of short-chain fatty acids or numbers of regulatory T cells. Notably, imipenem-cilastatin treatment of mice with GVHD led to loss of the protective mucus lining of the colon (P < 0.01) and the compromising of intestinal barrier function (P < 0.05). Sequencing of mouse stool specimens showed an increase in Akkermansia muciniphila (P < 0.001), a commensal bacterium with mucus-degrading capabilities, raising the possibility that mucus degradation may contribute to murine GVHD. We demonstrate an underappreciated risk for the treatment of allo-HSCT recipients with antibiotics that may exacerbate GVHD in the colon.
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Affiliation(s)
- Yusuke Shono
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa D. Docampo
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan U. Peled
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Medical College of Cornell University, New York, New York
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Suelen M. Perobelli
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Enrico Velardi
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Clinical and Experimental Medicine, University of Perugia, Perugia, Italy
| | - Jennifer J. Tsai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ann E. Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Odette M. Smith
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lauren F. Young
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jyotsna Gupta
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sophia R. Lieberman
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hillary V. Jay
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katya F. Ahr
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kori A. Porosnicu Rodriguez
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ke Xu
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marco Calarfiore
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hendrik Poeck
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Silvia Caballero
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Franck Rapaport
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jarrod A. Dudakov
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Alan M. Hanash
- Weill Medical College of Cornell University, New York, New York
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Boglarka Gyurkocza
- Weill Medical College of Cornell University, New York, New York
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - George F. Murphy
- Program in Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Camilla Gomes
- Program in Dermatopathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chen Liu
- Departments of Pathology and Laboratory Medicine, New Jersey Medical School and Robert Wood Johnson Medical School, Rutgers University, Newark, New Jersey
| | - Eli L. Moss
- Department of Medicine and Genetics, Stanford University, Stanford, California
| | - Shannon B. Falconer
- Department of Medicine and Genetics, Stanford University, Stanford, California
| | - Ami S. Bhatt
- Department of Medicine and Genetics, Stanford University, Stanford, California
| | - Ying Taur
- Weill Medical College of Cornell University, New York, New York
- Infectious Diseases Service, Lucille Castori Center for Microbes, Inflammation & Cancer, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric G. Pamer
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Medical College of Cornell University, New York, New York
- Infectious Diseases Service, Lucille Castori Center for Microbes, Inflammation & Cancer, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marcel R.M. van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Medical College of Cornell University, New York, New York
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert R. Jenq
- Weill Medical College of Cornell University, New York, New York
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Lyte M, Chapel A, Lyte JM, Ai Y, Proctor A, Jane JL, Phillips GJ. Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior. PLoS One 2016; 11:e0146406. [PMID: 26745269 PMCID: PMC4706316 DOI: 10.1371/journal.pone.0146406] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 10/26/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022] Open
Abstract
The increasing recognition that the gut microbiota plays a central role in behavior and cognition suggests that the manipulation of microbial taxa through diet may provide a means by which behavior may be altered in a reproducible and consistent manner in order to achieve a beneficial outcome for the host. Resistant starch continues to receive attention as a dietary intervention that can benefit the host through mechanisms that include altering the intestinal microbiota. Given the interest in dietary approaches to improve health, the aim of this study was to investigate whether the use of dietary resistant starch in mice to alter the gut microbiota also results in a change in behavior. Forty-eight 6 week-old male Swiss-Webster mice were randomly assigned to 3 treatment groups (n = 16 per group) and fed either a normal corn starch diet (NCS) or diets rich in resistant starches HA7 diet (HA7) or octenyl-succinate HA7 diet (OS-HA7) for 6 week and monitored for weight, behavior and fecal microbiota composition. Animals fed an HA7 diet displayed comparable weight gain over the feeding period to that recorded for NCS-fed animals while OS-HA7 displayed a lower weight gain as compared to either NCS or HA7 animals (ANOVA p = 0.0001; NCS:HA7 p = 0.244; HA7:OS-HA7 p<0.0001; NCS:OS-HA7 p<0.0001). Analysis of fecal microbiota using 16s rRNA gene taxonomic profiling revealed that each diet corresponded with a unique gut microbiota. The distribution of taxonomic classes was dynamic over the 6 week feeding period for each of the diets. At the end of the feeding periods, the distribution of taxa included statistically significant increases in members of the phylum Proteobacteria in OS-HA7 fed mice, while the Verrucomicrobia increased in HA7 fed mice over that of mice fed OS-HA7. At the class level, members of the class Bacilli decreased in the OS-HA7 fed group, and Actinobacteria, which includes the genus Bifidobacteria, was enriched in the HA7 fed group compared to the control diet. Behavioral analysis revealed that animals demonstrated profound anxiety-like behavior as observed by performance on the elevated-plus maze with time spent by the mice in the open arm (ANOVA p = 0.000; NCS:HA7 p = 0.004; NCS:OS-HA7 p = 1.000; HA7:OS-HA7 p = 0.0001) as well as entries in the open arm (ANOVA p = 0.039; NCS:HA7 p = 0.041; HA7:OS-HA7 p = 0.221; NCS:OS-HA7 p = 1.000). Open-field behavior, a measure of general locomotion and exploration, revealed statistically significant differences between groups in locomotion as a measure of transitions across quadrant boundaries. Additionally, the open-field assay revealed decreased exploration as well as decreased rearing in HA7 and OS-HA7 fed mice demonstrating a consistent pattern of increased anxiety-like behavior among these groups. Critically, behavior was not correlated with weight. These results indicate that diets based on resistant starch can be utilized to produce quantifiable changes in the gut microbiota and should be useful to "dial-in" a specific microbiome that is unique to a particular starch composition. However, undesirable effects can also be associated with resistant starch, including lack of weight gain and increased anxiety-like behaviors. These observations warrant careful consideration when developing diets rich in resistant starch in humans and animal models.
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Affiliation(s)
- Mark Lyte
- Department of Immunotherapeutics and Biotechnology, School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, Texas, 79606, United States of America
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Ashley Chapel
- School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, 79905, United States of America
| | - Joshua M. Lyte
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Yongfeng Ai
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Alexandra Proctor
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Jay-Lin Jane
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Gregory J. Phillips
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
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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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Elliott DR, Caporn SJM, Nwaishi F, Nilsson RH, Sen R. Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation. PLoS One 2015; 10:e0124726. [PMID: 25969988 PMCID: PMC4430338 DOI: 10.1371/journal.pone.0124726] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/04/2015] [Indexed: 02/01/2023] Open
Abstract
The UK hosts 15–19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.
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Affiliation(s)
- David R. Elliott
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- * E-mail:
| | - Simon J. M. Caporn
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
| | - Felix Nwaishi
- Cold Regions Research Centre, Wilfrid Laurier University, Waterloo, Ontario, 2NL 3C5, Canada
| | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30. Gothenburg, Sweden
| | - Robin Sen
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
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Figuerola ELM, Guerrero LD, Türkowsky D, Wall LG, Erijman L. Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale. Environ Microbiol 2015; 17:678-88. [PMID: 24803003 DOI: 10.1111/1462-2920.12497] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/28/2014] [Indexed: 11/28/2022]
Abstract
The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyse bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on β-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower β-diversity and narrower breadth compared with distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of β-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region was likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity.
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Affiliation(s)
- Eva L M Figuerola
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI-CONICET), Buenos Aires, Argentina
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Abstract
The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis. It consists of a core of phyla Planctomycetes, Verrucomicrobia and Chlamydiae, but several other phyla have been considered to be members, including phylum Lentisphaerae and several other phyla consisting only of yet-to-be cultured members. The genomics-based links between Planctomycetes, Verrucomicrobia and Chlamydiae have been recently strengthened, but there appear to be other features which may confirm the relationship at least of Planctomycetes, Verrucomicrobia and Lentisphaerae. Remarkably these include the unique planctomycetal compartmentalized cell plan differing from the cell organization typical for bacteria. Such a shared cell plan suggests that the common ancestor of the PVC superphylum members may also have been compartmentalized, suggesting this is an evolutionarily homologous feature at least within the superphylum. Both the PVC endomembranes and the eukaryote-homologous membrane-coating MC proteins linked to endocytosis ability in Gemmata obscuriglobus and shared by PVC members suggest such homology may extend beyond the bacteria to the Eukarya. If so, either our definition of bacteria may have to change or PVC members admitted to be exceptions. The cases for and against considering the PVC superphylum members as exceptions to the bacteria are discussed, and arguments for them as exceptions presented. Recent critical analysis has favoured convergence and analogy for explaining eukaryote-like features in planctomycetes and other PVC organisms. The case is made for constructing hypotheses leaving the possibility of homology and evolutionary links to eukaryote features open. As the case of discovery of endocytosis-like protein uptake in planctomycetes has suggested, this may prove a strong basis for the immediate future of experimental research programs in the PVC scientific community.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia,
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DeLorenzo S, Bräuer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P. Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing. PLoS One 2012; 7:e46695. [PMID: 23056406 PMCID: PMC3463544 DOI: 10.1371/journal.pone.0046695] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 01/08/2012] [Accepted: 09/06/2012] [Indexed: 11/25/2022] Open
Abstract
In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13)C-NaHCO(3), doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.
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Affiliation(s)
- Suzanne DeLorenzo
- Center for Coastal Margin Observation & Prediction and Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Beaverton, Oregon, United States of America.
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McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays 2011; 33:810-7. [PMID: 21858844 PMCID: PMC3795523 DOI: 10.1002/bies.201100045] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/13/2011] [Accepted: 07/15/2011] [Indexed: 11/11/2022]
Abstract
Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.
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Affiliation(s)
- James O McInerney
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
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