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He K, Xiong J, Yang W, Zhao L, Wang T, Qian W, Hu S, Wang Q, Aleem MT, Miao W, Yan W. Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets. Int J Mol Sci 2023; 24:10791. [PMID: 37445967 DOI: 10.3390/ijms241310791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Balantioides coli plays an important role in the diarrhea of weaned piglets, but its pathogenic potential and interaction with gut microbes remain unclear. To investigate the impact of B. coli colonization on the gut bacterial structure and function of weaned piglets, a metagenomic analysis based on shotgun sequencing was performed on fresh fecal samples collected from ten B. coli-colonized piglets and eight B. coli-free ones in this study. The results showed that decreasing diversity and shifted composition and function of the bacterial community were detected in the weaned piglets infected by B. coli. In contrast to the B. coli-negative group, the relative abundances of some members of the Firmicutes phylum including Clostridium, Ruminococcus species, and Intestinimonas butyriciproducens, which produce short-chain fatty acids, were significantly reduced in the B. coli-positive group. Notably, some species of the Prevotella genus (such as Prevotella sp. CAG:604 and Prevotella stercorea) were significantly increased in abundance in the B. coli-positive piglets. A functional analysis of the gut microbiota demonstrated that the differential gene sets for the metabolism of carbohydrates and amino acids were abundant in both groups, and the more enriched pathways in B. coli-infected piglets were associated with the sugar-specific phosphotransferase system (PTS) and the two-component regulatory system, as well as lipopolysaccharide (LPS) biosynthesis. Furthermore, several species of Prevotella were significantly positively correlated to the synthesis of lipid A, leading to the exporting of endotoxins and, thereby, inducing inflammation in the intestines of weaned piglets. Taken together, these findings revealed that colonization by B. coli was distinctly associated with the dysbiosis of gut bacterial structure and function in weaned piglets. Lower relative abundances of Clostridiaceae and Ruminococcaceae and higher abundances of Prevotella species were biomarkers of B. coli infection in weaned piglets.
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Affiliation(s)
- Kai He
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Lizhuo Zhao
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Tianqi Wang
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Suhui Hu
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Qiangqiang Wang
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Muhammad Tahir Aleem
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, Cleveland, OH 44115, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenchao Yan
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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2
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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3
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Larsen PE, Dai Y. Modeling interaction networks between host, diet, and bacteria predicts obesogenesis in a mouse model. Front Mol Biosci 2022; 9:1059094. [PMID: 36458093 PMCID: PMC9705962 DOI: 10.3389/fmolb.2022.1059094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 09/10/2024] Open
Abstract
Host-microbiome interactions are known to have substantial effects on human health, but the diversity of the human microbiome makes it difficult to definitively attribute specific microbiome features to a host phenotype. One approach to overcoming this challenge is to use animal models of host-microbiome interaction, but it must be determined that relevant aspects of host-microbiome interactions are reflected in the animal model. One such experimental validation is an experiment by Ridura et al. In that experiment, transplanting a microbiome from a human into a mouse also conferred the human donor's obesity phenotype. We have aggregated a collection of previously published host-microbiome mouse-model experiments and combined it with thousands of sequenced and annotated bacterial genomes and metametabolomic pathways. Three computational models were generated, each model reflecting an aspect of host-microbiome interactions: 1) Predict the change in microbiome community structure in response to host diet using a community interaction network, 2) Predict metagenomic data from microbiome community structure, and 3) Predict host obesogenesis from modeled microbiome metagenomic data. These computationally validated models were combined into an integrated model of host-microbiome-diet interactions and used to replicate the Ridura experiment in silico. The results of the computational models indicate that network-based models are significantly more predictive than similar but non-network-based models. Network-based models also provide additional insight into the molecular mechanisms of host-microbiome interaction by highlighting metabolites and metabolic pathways proposed to be associated with microbiome-based obesogenesis. While the models generated in this study are likely too specific to the animal models and experimental conditions used to train our models to be of general utility in a broader understanding of obesogenesis, the approach detailed here is expected to be a powerful tool of investigating multiple types of host-microbiome interactions.
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Affiliation(s)
- Peter E. Larsen
- Loyola Genomics Facility, Loyola University at Chicago Health Science Campus, Maywood, IL, United States
| | - Yang Dai
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, United States
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4
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Mohsin Bukhari S, Ahmed Alghamdi H, Ur Rehman K, Andleeb S, Ahmad S, Khalid N. Metagenomics analysis of the fecal microbiota in Ring-necked pheasants ( Phasianus colchicus) and Green pheasants ( Phasianus versicolor) using next generation sequencing. Saudi J Biol Sci 2022; 29:1781-1788. [PMID: 35280539 PMCID: PMC8913415 DOI: 10.1016/j.sjbs.2021.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022] Open
Abstract
Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.
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Affiliation(s)
- Syed Mohsin Bukhari
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Khalil Ur Rehman
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahla Andleeb
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahbaz Ahmad
- Department of Entomology, University of the Punjab, 54590 Lahore, Pakistan
| | - Nimra Khalid
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
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5
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Panaiotov S, Hodzhev Y, Tsafarova B, Tolchkov V, Kalfin R. Culturable and Non-Culturable Blood Microbiota of Healthy Individuals. Microorganisms 2021; 9:1464. [PMID: 34361900 PMCID: PMC8304615 DOI: 10.3390/microorganisms9071464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.
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Affiliation(s)
- Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Yordan Hodzhev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Borislava Tsafarova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Vladimir Tolchkov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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6
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Nousias O, Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics 2021; 59:100866. [PMID: 33812777 DOI: 10.1016/j.margen.2021.100866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Microbial communities play fundamental roles in association with marine algae; in fact, they are recognized to be actively involved in growth and morphogenesis of the algae. Porphyra purpurea is a red alga commonly found in the intertidal zone with a high economic value, however little is known about the bacterial species associated with this genus. Here we report the bacterial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets. These were analyzed with Methaplan3 to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared these results to the 16S rRNA metagenomic analysis pipeline of the MGnify database to evaluate both methods. Kraken2 was used to verify and support the results, as a complementary classification method to Metaphlan3. This approach highlighted the different taxonomic resolution of a 16S rRNA OTU-based method compared to the pan-genome approach deployed by Metaphlan3 and complemented by Kraken2. The results presented here provide valuable preliminary data on the putative host-associated bacterial species of P. purpurea.
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Affiliation(s)
- Orestis Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece; Department of Biology, University of Crete, Greece.
| | - Federica Montesanto
- Department of Biology, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy; CoNISMa, Piazzale Flaminio 9, 00197 Roma, Italy.
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7
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Yang Y, Li X, Cao Z, Qiao Y, Lin Q, Liu J, Zhao Z, An Q, Zhang C, Zhang H, Pan H. Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers. Pol J Microbiol 2021; 70:33-43. [PMID: 33815525 PMCID: PMC8008768 DOI: 10.33073/pjm-2021-001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/24/2020] [Accepted: 12/27/2020] [Indexed: 12/25/2022] Open
Abstract
Short-term or acute temperature stress affect the immune responses and alters the gut microbiota of broilers, but the influences of long-term temperature stress on stress biomarkers and the intestinal microbiota remains largely unknown. Therefore, we examined the effect of three long-term ambient temperatures (high (HC), medium (MC), and low (LC) temperature groups) on the gene expression of broilers’ heat shock proteins (Hsps) and inflammation – related genes, as well as the caecal microbial composition. The results revealed that Hsp70 and Hsp90 levels in HC group significantly increased, and levels of Hsp70, Hsp90, IL-6, TNF-α, and NFKB1 in LC group were significantly higher than in MC group (p < 0.05). In comparison with the MC group, the proportion of Firmicutes increased in HC and LC groups, while that of Bacteroidetes decreased in LC group at phylum level (p < 0.05). At genus level, the proportion of Escherichia/Shigella, Phascolarctobacterium, Parabacteroides,and Enterococcus increased in HC group; the fraction of Faecalibacterium was higher in LC group; and the percentage of Barnesiella and Alistipes decreased in both HC and LC groups (p < 0.05). Functional analysis based on communities’ phylogenetic investigation revealed that the pathways involved in environmental information processing and metabolism were enriched in the HC group. Those involved in cellular processes and signaling, metabolism, and gene regulation were enriched in LC group. Hence, we conclude that the long-term temperature stress can greatly alter the intestinal microbial communities in broilers and may further affect the host’s immunity and health.
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Affiliation(s)
- Yuting Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Xing Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Zhenhui Cao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Yinging Qiao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Qiuye Lin
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Jianping Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, The People's Republic of China
| | - Zhiyong Zhao
- Yunnan Animal Science and Veterinary Institute, Kunming, The People's Republic of China
| | - Qingcong An
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Chunyong Zhang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
| | - Hongfu Zhang
- Institute of Animal Science Chinese Academy of Agricultural Sciences, Beijing, The People's Republic of China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, The People's Republic of China
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8
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Deep Learning for Integrated Analysis of Insulin Resistance with Multi-Omics Data. J Pers Med 2021; 11:jpm11020128. [PMID: 33671853 PMCID: PMC7918166 DOI: 10.3390/jpm11020128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/25/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Technological advances in next-generation sequencing (NGS) have made it possible to uncover extensive and dynamic alterations in diverse molecular components and biological pathways across healthy and diseased conditions. Large amounts of multi-omics data originating from emerging NGS experiments require feature engineering, which is a crucial step in the process of predictive modeling. The underlying relationship among multi-omics features in terms of insulin resistance is not well understood. In this study, using the multi-omics data of type II diabetes from the Integrative Human Microbiome Project, from 10,783 features, we conducted a data analytic approach to elucidate the relationship between insulin resistance and multi-omics features, including microbiome data. To better explain the impact of microbiome features on insulin classification, we used a developed deep neural network interpretation algorithm for each microbiome feature’s contribution to the discriminative model output in the samples.
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Lu Z, Ji C, Luo X, Lan Y, Han L, Chen Y, Liu X, Lin Q, Lu F, Wu X, Guo R, Zou C. Nanoparticle-Mediated Delivery of Emodin via Colonic Irrigation Attenuates Renal Injury in 5/6 Nephrectomized Rats. Front Pharmacol 2021; 11:606227. [PMID: 33551808 PMCID: PMC7858270 DOI: 10.3389/fphar.2020.606227] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/08/2020] [Indexed: 11/13/2022] Open
Abstract
Our previous study showed that emodin enema modulates gut microbiota and delays CKD progression. However, the poor solubility, limited colonic irrigation retention time, and inadequate colon adhesion of emodin hinder its clinical application. Based on the deficiencies of emodin, we prepared monomethoxy-poly (ethylene glycol)-poly (lactic acid)-chitosan-2-mercaptobenzimidazole nanoparticles with incorporated emodin (emodin-NP) and studied their efficacy in delaying CKD progression. 5/6 nephrectomized Male Sprague Dawley rats were administered via colonic irrigation with emodin-NP every two days for eight weeks. We found that treatment with emodin-NP improved the kidney function of the rats and limited the expansion of tubulointerstitial fibrosis. Treatment with emodin-NP once every two days is comparable to emodin treatment once a day. Furthermore, emodin-NP via colonic irrigation remarkably reduced IL-1β, IL-6, and LPS levels in serum, improved intestinal barrier functions, and downregulated the key proteins (TLR4, MyD88, and NF-κB) expression in intestinal TLR4 signaling pathway. 16S rDNA analyses showed that emodin-NP can regulate microbiota disturbance in CKD. Taken together, these results suggest that emodin-NP alleviates kidney dysfunction and tubulointerstitial fibrosis by mediation through the modification of gut microbiota disorders. Emodin-NP may be a new method to treat CKD.
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Affiliation(s)
- Zhaoyu Lu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Chunlan Ji
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuewen Luo
- Department of Nephrology, The Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yong Lan
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Lijuan Han
- Department of Bioinformatics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yang Chen
- Department of Bioinformatics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xusheng Liu
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qinzhan Lin
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Fuhua Lu
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiuqing Wu
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Rui Guo
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Chuan Zou
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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10
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Yang Y, Gao H, Li X, Cao Z, Li M, Liu J, Qiao Y, Ma L, Zhao Z, Pan H. Correlation analysis of muscle amino acid deposition and gut microbiota profile of broilers reared at different ambient temperatures. Anim Biosci 2020; 34:93-101. [PMID: 32898964 PMCID: PMC7888499 DOI: 10.5713/ajas.20.0314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023] Open
Abstract
Objective Temperature could influence protein and amino acid deposition as well as gut microbiota profile and composition. However, the specific effects of ambient temperature on amino acids deposition and gut microbiota composition remain insufficiently understood. Methods A total of 300 one-day-old Avian broilers were randomly divided into three groups and reared at high, medium, and low temperature (HT, MT, and LT), respectively. Breast muscle and fecal samples were collected for amino acid composition analysis and 16S rRNA gene sequence analysis. Results Our data showed that compared to the MT group, there was a decrease of muscle leucine and tyrosine (p<0.05), as well as an increase of methionine in the HT group (p<0.05) and a decrease of serine in the LT group. Examination of microbiota shift revealed that at genus level, the relative abundance of Turicibacter and Parabacteroides was increased in the HT group (p<0.05) and that the relative abundances of Pandoraea, Achromobacter, Prevotella, Brevundimonas, and Stenotrophomonas in the LT group were higher than those in the MT group (p<0.05). In addition, there were substantial correlations between microbes and amino acids. In the HT group. Turicibacter was negatively correlated with aspartic acid and tyrosine, whereas Parabacteroides was positively correlated with methionine (p<0.05). In the LT group, there were multiple positive correlations between Achromobacter and arginine, isoleucine or tyrosine; between Prevotella and cysteine or phenylalanine; between Brevundimonas and cysteine; and between Stenotrophomonas and cysteine as well as a negative correlation between Stenotrophomonas and serine. Conclusion Our findings demonstrated that amino acid content of breast muscle and intestinal microbiota profile was affected by different ambient temperatures. Under heat exposure, augmented abundance of Parabacteroides was correlated with elevated methionine. Low temperature treatment may affect muscle tyrosine content through the regulation of Achromobacter.
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Affiliation(s)
- Yuting Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
| | - Huan Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
| | - Xing Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
| | - Zhenhui Cao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
| | - Meiquan Li
- Department of Animal Husbandry and Veterinary Medicine, College of Agriculture, Kunming University, Kunming 650201, China
| | - Jianping Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yingying Qiao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
| | - Li Ma
- Yunnan Vocational and Technical College of Agriculture, Kunming 650201, China
| | - Zhiyong Zhao
- Yunnan Animal Science and Veterinary Institute, Kunming 650201, China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201 China
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11
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Pan Y, Wan X, Zeng F, Zhong R, Guo W, Lv XC, Zhao C, Liu B. Regulatory effect of Grifola frondosa extract rich in polysaccharides and organic acids on glycolipid metabolism and gut microbiota in rats. Int J Biol Macromol 2020; 155:1030-1039. [DOI: 10.1016/j.ijbiomac.2019.11.067] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
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12
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The Role of Arginine in Disease Prevention, Gut Microbiota Modulation, Growth Performance and the Immune System of Broiler Chicken – A Review. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The effect of dietary arginine on disease prevention, immune system modulation, the gut micro-biota composition and growth of broiler chicken was reviewed. The main aim of poultry production is the maximization of profit at the least possible cost. This objective can mainly be achieved by ensuring that there is no interference in growth or disease outbreak and by feeding chicken with the best possible level of nutrients. With the ban on antibiotic growth promoters, attention is shifted towards other nutrition methods to prevent diseases and promote growth. More attention is therefore given to protein diets in animal nutrition due to their importance as essential part of active biological compounds in the body, assisting in the breakdown of body tissue and helping in the physiological processes of the animal. Arginine plays important function in serving as building blocks of proteins and polypeptides. It performs other roles during the regulation of important biochemical functions such as maintenance, growth, reproduction and immunity. Arginine cannot be synthesized by the body so it has to be supplemented in the diet. When arginine is supplemented above the recommended level, the gut mucosa is protected, immunosuppression is alleviated, diseases like necrotic enteritis, infectious bursal disease and coccidiosis in broiler chickens are prevented. There is an improvement in growth resulting from the increase in intestinal absorption, barrier function and microbiota composition.
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13
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Hu X, Du J, Xie Y, Huang Q, Xiao Y, Chen J, Yan S, Gong Z, Ouyang S. Fecal microbiota characteristics of Chinese patients with primary IgA nephropathy: a cross-sectional study. BMC Nephrol 2020; 21:97. [PMID: 32169051 PMCID: PMC7071635 DOI: 10.1186/s12882-020-01741-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Growing evidence has shown that the gut-renal connection and gut microbiota dysbiosis play a critical role in immunoglobulin A nephropathy (IgAN). However, the fecal microbiome profile in Chinese patients with IgAN remains unknown. A cross-sectional study was designed for the first time to investigate the fecal microbiota compositions in patients with primary IgAN in China and to evaluate the relationship between the fecal microbiome and IgAN clinical presentation. METHODS Fecal samples were collected from 17 IgAN patients and 18 age-, sex-, and body mass index-matched healthy controls, and bacterial DNA was extracted for 16S ribosomal RNA gene sequencing targeting the V3-V4 region. RESULTS Fecal samples from the IgAN patients and healthy controls showed differences in gut microbiota community richness and compositions. Compared to the healthy controls, IgAN patients at the phylum level had an increased abundance of Fusobacteria, but a decreased abundance of Synergistetes. The significantly increased genera in the IgAN group were Escherichia-Shigella, Hungatella, and Eggerthella, all of which possess pathogenic potential. Furthermore, the genus Escherichia-Shigella was negatively associated with the estimated glomerular filtration rate (eGFR) but was positively associated with the urinary albumin-to-creatinine ratio (uACR). However, the genus rectale_group was present in the IgAN group with a low abundance and was negatively associated with the uACR. Functional analysis disclosed that infection-related pathways were enriched in the IgAN group. CONCLUSIONS We demonstrate that gut microbiota dysbiosis occurs in patients with IgAN, and that changes in gut bacterial populations are closely related to IgAN clinical features, suggesting that certain specific gut microbiota may be a potential therapeutic target for IgAN.
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Affiliation(s)
- Xiaofang Hu
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China
| | - Jie Du
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China
| | - Yuhong Xie
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China
| | - Qiong Huang
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China
| | - Yi Xiao
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China
| | - Juan Chen
- Department of Nephrology, Hunan Provincial People's Hospital, The first-affiliated hospital of Hunan normal university, No. 61 Jie-fang West Road, Fu-Rong District, Changsha, 410005, Hunan, China
| | - Siyuan Yan
- Department of Nephrology, Hunan Provincial People's Hospital, The first-affiliated hospital of Hunan normal university, No. 61 Jie-fang West Road, Fu-Rong District, Changsha, 410005, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Kaifu District, Changsha, 410008, Hunan, China.
| | - Shaxi Ouyang
- Department of Nephrology, Hunan Provincial People's Hospital, The first-affiliated hospital of Hunan normal university, No. 61 Jie-fang West Road, Fu-Rong District, Changsha, 410005, Hunan, China.
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14
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Aljahdali N, Gadonna-Widehem P, Anton PM, Carbonero F. Gut Microbiota Modulation by Dietary Barley Malt Melanoidins. Nutrients 2020; 12:nu12010241. [PMID: 31963440 PMCID: PMC7019678 DOI: 10.3390/nu12010241] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 01/27/2023] Open
Abstract
Melanoidins are the final Maillard reaction products (protein–carbohydrate complexes) produced in food by prolonged and intense heating. We assessed the impact of the consumption of melanoidins from barley malts on gut microbiota. Seventy-five mice were assigned into five groups, where the control group consumed a non-melanoidin malt diet, and other groups received melanoidin-rich malts in increments of 25% up to 100% melanoidin malts. Feces were sampled at days 0, 1, 2, 3, 7, 14, and 21 and the microbiota was determined using V4 bacterial 16S rRNA amplicon sequencing and short-chain fatty acids (SCFA) by gas chromatography. Increased melanoidins was found to result in significantly divergent gut microbiota profiles and supported sustained SCFA production. The relative abundance of Dorea, Oscillibacter, and Alisitpes were decreased, while Lactobacillus, Parasutterella, Akkermansia, Bifidobacterium, and Barnesiella increased. Bifidobacterium spp. and Akkermansia spp. were significantly increased in mice consuming the highest melanoidin amounts, suggesting remarkable prebiotic potential.
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Affiliation(s)
- Nesreen Aljahdali
- Department of Biological Science, King Abdulaziz University, Jeddah 21551, Saudi Arabia;
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Pascale Gadonna-Widehem
- Transformations et Agro-Ressources—EA7519-Institut Polytechnique UniLaSalle, 60026 Beauvais, France; (P.G.-W.); (P.M.A.)
| | - Pauline M. Anton
- Transformations et Agro-Ressources—EA7519-Institut Polytechnique UniLaSalle, 60026 Beauvais, France; (P.G.-W.); (P.M.A.)
| | - Franck Carbonero
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
- Department of Nutrition and Excercise Physiology, Elson Floyd School of Medicine, Washington State University-Spokane, 412 East Spokane Falls Boulevard, Spokane, WA 99202, USA
- Correspondence:
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15
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Wang L, Zhang Y, Fan G, Ren JN, Zhang LL, Pan SY. Effects of orange essential oil on intestinal microflora in mice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:4019-4028. [PMID: 30729524 DOI: 10.1002/jsfa.9629] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The intestinal microbiota has a wide variety of functions in the host. A positive effect of plant extract on intestinal microbiota in animals has been reported. However, the effect of orange essential oil and its components limonene, linalool and citral on intestinal microflora in mice has seldom been reported. The effects of intragastric administration of orange essential oil and limonene, linalool and citral on intestinal microflora and biochemical indexes in mice were studied. RESULTS The effect of essential oil, linalool and citral on immune organ index (spleen and thymus index), IgM and IL-2 was not significant (P > 0.05). A significant increase (P < 0.05) of H+ K+ -ATPase activity, IgA, IgG, and IL-2 in the limonene group was observed when compared with the control group. Orange essential oil, limonene, linalool and citral could significantly reduce the content of short-chain fatty acids in the cecum and colon of mice. Principal coordinates analysis showed that intestinal bacterial structure of limonene group cecum and colon was apparently separated from other groups. The relative abundance of Lactobacillus in cecum and colon in essential oil, limonene, linalool and citral groups was higher than that in the control group. CONCLUSIONS Orange essential oil and limonene, linalool and citral could affect the intestinal microflora of mice, and enhance the relative abundance of Lactobacillus. The intestinal bacterial structure of cecum and colon in the limonene group was quite different from other groups. This indicated a more obvious effect of limonene on intestinal bacteria, also resulting in significant changes in blood immune index and short-chain fatty acids in mice. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yan Zhang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gang Fan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing-Nan Ren
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lu-Lu Zhang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Si-Yi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Department of Food Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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16
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Abstract
The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome.
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17
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Abstract
The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome.
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18
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Gu J, Thomas-Ahner JM, Riedl KM, Bailey MT, Vodovotz Y, Schwartz SJ, Clinton SK. Dietary Black Raspberries Impact the Colonic Microbiome and Phytochemical Metabolites in Mice. Mol Nutr Food Res 2019; 63:e1800636. [PMID: 30763455 DOI: 10.1002/mnfr.201800636] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/26/2018] [Indexed: 12/11/2022]
Abstract
SCOPE Black raspberries (BRB) are a rich source of bioactive phytochemicals, including anthocyanins and ellagitannins. These phytochemicals are poorly absorbed and may be transformed by gut microbiota into various metabolites that may impact the colonic mucosa or upon absorption have systemic bioactivity. The objective of this study is to define the impact of a BRB-containing diet on the colon microbiome in mice and quantify the phytochemical metabolites in the colon contents and circulation. METHODS AND RESULTS Male mice were fed 10% w/w freeze-dried BRB powder for 6 weeks. The colonic microbiota was evaluated by 16S rRNA gene sequencing. Anthocyanin and ellagitannin metabolites, protocatechuic acid, and urolithins were analyzed by HPLC-MS/MS. The BRB diet impacted colon mucosal microbial composition with a more robust effect observed on the luminal microflora. BRB-derived protocatechuic acid and urolithins were quantified in the colon, luminal contents, plasma, liver, and prostate with protocatechuic acid present in higher concentrations compared to urolithins. CONCLUSION This study highlights the complex interactions between dietary phytochemicals, the host microbiome, and metabolism. It is demonstrated that microbially produced phytochemical metabolites are present in the colon and systemic circulation where they may exert biological activity.
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Affiliation(s)
- Junnan Gu
- Interdisciplinary PhD Program in Nutrition, The Ohio State University, Columbus, 43210, OH, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA
| | | | - Kenneth M Riedl
- Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.,Department of Food Science and Technology, The Ohio State University, Columbus, 43210, OH, USA.,Nutrient & Phytochemical Analytic Shared Resource, The Ohio State University, Columbus, 43210, OH, USA
| | - Michael T Bailey
- Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.,Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, 43205, OH, USA.,Institute for Behavioral Medicine Research, The Ohio State University, Columbus, 43210, OH, USA
| | - Yael Vodovotz
- Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.,Department of Food Science and Technology, The Ohio State University, Columbus, 43210, OH, USA
| | - Steven J Schwartz
- Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.,Department of Food Science and Technology, The Ohio State University, Columbus, 43210, OH, USA.,Nutrient & Phytochemical Analytic Shared Resource, The Ohio State University, Columbus, 43210, OH, USA
| | - Steven K Clinton
- Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, 43210, OH, USA
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19
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Nuli R, Cai J, Kadeer A, Zhang Y, Mohemaiti P. Integrative Analysis Toward Different Glucose Tolerance-Related Gut Microbiota and Diet. Front Endocrinol (Lausanne) 2019; 10:295. [PMID: 31191448 PMCID: PMC6546033 DOI: 10.3389/fendo.2019.00295] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/24/2019] [Indexed: 12/17/2022] Open
Abstract
Objective: There is evidence that type 2 diabetes (T2DM) is affected by gut microbiota, and gut microbiota diversity modified by diet. To investigate its modifications in Uyghur patients with different glucose tolerance, we enrolled 561 subjects: newly diagnosed T2DM (n = 145), impaired glucose regulation (IGR) patients (n = 138) and in normal control (NC) population (n = 278). Methods: The nutrient intake in food frequency questionnaire was calculated by R language. The regions V3-V4 of 16S ribosomal RNA were sequenced by using Illumina Miseq platform. Sequences were clustered by operational taxonomy units, gut microbiota composition, and diversity was analyzed. Correlations between bacterial composition at different level and dietary factors were evaluated. Results: The α-diversity was highest in NC, followed by T2DM and IGR; β-diversity distinguished between patients and NC. Compared to NC, Saccharibacteria was significantly increased in T2DM and IGR. Deferribacteres was significantly increased in T2DM compared to NC and IGR. Veillonella, Pasteurellaceae, and Haemophilus were over-represented in IGR. Abundance of Bacteroidetes was negatively correlated with LDL-C; Abundance of Tenericutes was negatively correlated with hip circumference and total cholesterol, positively correlated with HDL-C and cake intake; Actinobacteria was positively correlated with BMI and folic acid intake, negatively correlated with oil intake. Firmicutes was negatively correlated with beverage and alcohol intake. Spirochaetae was negatively correlated with fungus, fruits, beans, vitamin C, dietary fiber, and calcium. Fusobacteria was positively correlated with beans intake, and was negatively correlated with fat intake. Proteobacteria was positively correlated with tuber crops intake. Synergistetes was positively correlated with cholesterol, nicotinic acid, and selenium intake. Deferribacteres was negatively correlated with magnesium intake. Conclusions: At the phylum and genus level, the structure and diversity of intestinal microbiota of T2DM and IGR was altered, the number of OTUs, the relative abundance, and diversity were all decreased. The gut microbiota of the newly diagnosed T2DM, IGR, and NC were related to age, blood lipids, BMI, blood pressure, and dietary nutrient intake. Unbalanced nutrient intake in the three groups may affect the structure and abundance of the gut microbiota, which may play a role in the occurrence and development of T2DM.
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Affiliation(s)
- Rebiya Nuli
- School of Public Health, Xinjiang Medical University, Ürümqi, China
- College of Basic Medical Science, Xinjiang Medical University, Ürümqi, China
| | - Junxiu Cai
- Medical Department, The Fifth Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | | | - Yangyi Zhang
- Health Management Institute, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Patamu Mohemaiti
- School of Public Health, Xinjiang Medical University, Ürümqi, China
- *Correspondence: Patamu Mohemaiti
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20
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Mahnic A, Rupnik M. Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort. PLoS One 2018; 13:e0209209. [PMID: 30571698 PMCID: PMC6301613 DOI: 10.1371/journal.pone.0209209] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/30/2018] [Indexed: 01/26/2023] Open
Abstract
Gut microbiota in a healthy population is shaped by various geographic, demographic and lifestyle factors. Although the majority of research remains focused on the bacterial community, recent efforts to include the remaining microbial members like viruses, archaea and especially fungi revealed various functions they perform in the gut. Using the amplicon sequencing approach we analysed bacterial and fungal gut communities in a Slovenian cohort of 186 healthy volunteers. In the bacterial microbiome we detected 253 different genera. A core microbiome analysis revealed high consistency with previous studies, most prominently showing that genera Faecalibacterium, Bacteroides and Roseburia regularly comprise the core community. We detected a total of 195 fungal genera, but the majority of these showed low prevalence and are likely transient foodborne contaminations. The fungal community showed a low diversity per sample and a large interindividual variability. The most abundant fungi were Saccharomyces cerevisiae and Candida albicans. These, along with representatives from genera Penicillium and Debaryomyces, cover 82% of obtained reads. We report three significant questionnaire-based host covariates associated with microbiota composition. Bacterial community was associated with age and gender. More specifically, bacterial diversity was increased with age and was higher in the female population compared to male. The analysis of fungal community showed that more time dedicated to physical activity resulted in a higher fungal diversity and lower abundance of S. cerevisiae. This is likely dependent on different diets, which were reported by participants according to the respective rates of physical activity.
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Affiliation(s)
- Aleksander Mahnic
- Department for Microbiological Research, National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Maja Rupnik
- Department for Microbiological Research, National Laboratory for Health, Environment and Food, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- * E-mail:
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21
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Ashaolu TJ, Saibandith B, Yupanqui CT, Wichienchot S. Human colonic microbiota modulation and branched chain fatty acids production affected by soy protein hydrolysate. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13916] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Bandhita Saibandith
- Interdisciplinary Graduate School of Nutraceutical and Functional Food (IGS-NFF); Prince of Songkla University; Hat Yai, Songkhla 90112 Thailand
| | - Chutha Takahashi Yupanqui
- Interdisciplinary Graduate School of Nutraceutical and Functional Food (IGS-NFF); Prince of Songkla University; Hat Yai, Songkhla 90112 Thailand
| | - Santad Wichienchot
- Interdisciplinary Graduate School of Nutraceutical and Functional Food (IGS-NFF); Prince of Songkla University; Hat Yai, Songkhla 90112 Thailand
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22
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Behzad H, Mineta K, Gojobori T. Global Ramifications of Dust and Sandstorm Microbiota. Genome Biol Evol 2018; 10:1970-1987. [PMID: 29961874 PMCID: PMC6097598 DOI: 10.1093/gbe/evy134] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.
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Affiliation(s)
- Hayedeh Behzad
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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Williams NC, Killer SC, Svendsen IS, Jones AW. Immune nutrition and exercise: Narrative review and practical recommendations. Eur J Sport Sci 2018; 19:49-61. [PMID: 29975589 DOI: 10.1080/17461391.2018.1490458] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Evidence suggests that periods of heavy intense training can result in impaired immune cell function, and whether this leaves elite athletes at greater risk of infections and upper respiratory symptoms (URS) is still debated. There is some evidence that episodes of URS do cluster around important periods of competition and intense periods of training. Since reducing URS, primarily from an infectious origin, may have implications for performance, a large amount of research has focused on nutritional strategies to improve immune function at rest and in response to exercise. Although there is some convincing evidence that meeting requirements of high intakes in carbohydrate and protein and avoiding deficiencies in nutrients such as vitamin D and antioxidants is integral for optimal immune health, well-powered randomised controlled trials reporting improvements in URS beyond such intakes are lacking. Consequently, there is a need to first understand whether the nutritional practices adopted by elite athletes increases their risk of URS. Second, promising evidence in support of efficacy and mechanisms of immune-enhancing nutritional supplements (probiotics, bovine colostrum) on URS needs to be followed up with more randomised controlled trials in elite athletes with sufficient participant numbers and rigorous procedures with clinically relevant outcome measures of immunity.
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Affiliation(s)
- Neil C Williams
- a Exercise and Health Research Group, Department of Sport Science, School of Science and Technology , Nottingham Trent University , Nottingham , UK
| | - Sophie C Killer
- b British Athletics, English Institute of Sport, National Performance Institute, Loughborough University , Loughborough , UK
| | | | - Arwel Wyn Jones
- d Lincoln Institute for Health, University of Lincoln , Lincoln , UK
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24
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Bacteriophages of the Urinary Microbiome. J Bacteriol 2018; 200:JB.00738-17. [PMID: 29378882 DOI: 10.1128/jb.00738-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/11/2018] [Indexed: 01/01/2023] Open
Abstract
Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.
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Wei X, Tao J, Xiao S, Jiang S, Shang E, Zhu Z, Qian D, Duan J. Xiexin Tang improves the symptom of type 2 diabetic rats by modulation of the gut microbiota. Sci Rep 2018; 8:3685. [PMID: 29487347 PMCID: PMC5829262 DOI: 10.1038/s41598-018-22094-2] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM), a chronic metabolic disease which severely impairs peoples' quality of life, currently attracted worldwide concerns. There are growing evidences that gut microbiota can exert a great impact on the development of T2DM. Xiexin Tang (XXT), a traditional Chinese medicine prescription, has been clinically used to treat diabetes for thousands of years. However, few researches are investigated on the modulation of gut microbiota community by XXT which will be very helpful to unravel how it works. In this study, bacterial communities were analyzed based on high-throughput 16S rRNA gene sequencing. Results indicated that XXT could notably shape the gut microbiota. T2DM rats treated with XXT exhibited obvious changes in the composition of the gut microbiota, especially for some short chain fatty acids producing and anti-inflammatory bacteria such as Adlercreutzia, Alloprevotella, Barnesiella, [Eubacterium] Ventriosum group, Blautia, Lachnospiraceae UCG-001, Papillibacter and Prevotellaceae NK3B31 group. Additionally, XXT could also significantly ameliorate hyperglycemia, lipid metabolism dysfunction and inflammation in T2DM rats. Moreover, the correlation analysis illustrated that the key microbiota had a close relationship with the T2DM related indexes. The results probably provided useful information for further investigation on its active mechanism and clinical application.
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Affiliation(s)
- Xiaoyan Wei
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Jinhua Tao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Suwei Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China.
| | - Erxin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, PR China.
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Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. MICROBIOME 2017; 5:20. [PMID: 28187782 PMCID: PMC5303297 DOI: 10.1186/s40168-017-0234-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/24/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution. RESULTS Here, we show that untargeted metagenomic sequencing of sputum DNA can provide valuable information beyond the possibilities of culture-based diagnosis. We sequenced the sputum of six CF patients and eleven control samples (including healthy subjects and chronic obstructive pulmonary disease patients) without prior depletion of human DNA or cell size selection, thus obtaining the most unbiased and comprehensive characterization of CF respiratory tract microbes to date. We present detailed descriptions of the CF and healthy lung microbiome, reconstruct near complete pathogen genomes, and confirm that the CF lungs consistently exhibit reduced microbial diversity. Crucially, the obtained genomic sequences enabled a detailed identification of the exact pathogen strain types, when analyzed in conjunction with existing multi-locus sequence typing databases. We also detected putative pathogenicity islands and indicators of antibiotic resistance, in good agreement with independent clinical tests. CONCLUSIONS Unbiased sputum metagenomics provides an in-depth profile of the lung pathogen microbiome, which is complementary to and more detailed than standard culture-based reporting. Furthermore, functional and taxonomic features of the dominant pathogens, including antibiotics resistances, can be deduced-supporting accurate and non-invasive clinical diagnosis.
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Affiliation(s)
- Rounak Feigelman
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christian R. Kahlert
- Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, St. Gallen, Switzerland
- Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Florent Baty
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Frank Rassouli
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Rebekka L. Kleiner
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Philipp Kohler
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Martin H. Brutsche
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
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Liu C, Huang D, Zhang W. Combining culture‐dependent and culture‐independent molecular methods for the isolation and purification of a potentially novel anaerobic species from pit mud in a Chinese liquor distillery. JOURNAL OF THE INSTITUTE OF BREWING 2016. [DOI: 10.1002/jib.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Chaolan Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics Chengdu University Chengdu 610052 China
- College of Light Industry, Textile and Food Engineering Sichuan University Chengdu 610065 China
| | - Dan Huang
- College of Light Industry, Textile and Food Engineering Sichuan University Chengdu 610065 China
| | - Wenxue Zhang
- College of Light Industry, Textile and Food Engineering Sichuan University Chengdu 610065 China
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Abstract
Global climate change can alter the distribution of microbial pathogens and vectors that transmit infectious diseases, exposing humans to newly emerging or reemerging diseases. Early detection of potential pathogens and vectors in the environment can facilitate upstream interventions that limit the spread of infectious disease. Metagenomics is the analysis of DNA sequences from a population of microorganisms in a particular environment, followed by the computational reconstruction of the data to determine what organisms are present and predict their role in the environment. Defining the microbial populations associated with humans, animals, and their environment provides insight into the structure of microbial communities in any particular niche, including the abundance, diversity, and composition of the microbes and viruses present. It can also reveal the distribution of virulence genes within that niche. These data can be used to identify reservoirs of pathogens in an environment and predict environments with a high probability for evolution of new pathogens or outbreaks caused by known pathogens, thereby facilitating approaches to prevent infections of animals or humans before serious outbreaks of infectious disease.
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Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens. J Clin Microbiol 2015; 54:368-75. [PMID: 26637379 DOI: 10.1128/jcm.01965-15] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/23/2015] [Indexed: 12/16/2022] Open
Abstract
The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing (r(2) = -0.60) and MSS (r(2) = -0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge.
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Fond G, Chevalier G, Eberl G, Leboyer M. [The potential role of microbiota in major psychiatric disorders: Mechanisms, preclinical data, gastro-intestinal comorbidities and therapeutic options]. Presse Med 2015; 45:7-19. [PMID: 26653939 DOI: 10.1016/j.lpm.2015.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/10/2015] [Accepted: 10/29/2015] [Indexed: 12/21/2022] Open
Abstract
While forecasts predict an increase in the prevalence of mental health disorders in the worldwide general population, the response rate to classical psychiatric treatment remains unsatisfactory. Resistance to psychotropic drugs can be due to clinical, pharmacological, pharmacokinetic, and pharmacodynamic factors. Among these factors, recent animal findings suggest that microbiota may have an underestimated influence on its host's behavior and on drug metabolism that may explain ineffectiveness or increased side effects of psychiatric medications such as weight gain. The following issues were identified in the present review: (i) microbiota dysbiosis and putative consequences on central nervous system functioning; (ii) chronic microbiota dysbiosis-associated illnesses in humans; (iii) microbiota-oriented treatments and their potential therapeutic applications in psychiatry.
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Affiliation(s)
- Guillaume Fond
- Inserm U955, équipe 15, université Paris-Est, fondation FondaMental, fondation de coopération scientifique, AP-HP, groupe hospitalo-universitaire Mondor, DHU Pe-Psy, hôpital A.-Chenevier, pôle de psychiatrie et d'addictologie, pavillon Hartmann, 40, rue de Mesly, 94000 Créteil, France.
| | - Grégoire Chevalier
- Institut Pasteur, unité de développement du tissu lymphoïde, 25, rue du Dr-Roux, 75724 Paris, France
| | - Gerard Eberl
- Institut Pasteur, unité de développement du tissu lymphoïde, 25, rue du Dr-Roux, 75724 Paris, France
| | - Marion Leboyer
- Inserm U955, équipe 15, université Paris-Est, fondation FondaMental, fondation de coopération scientifique, AP-HP, groupe hospitalo-universitaire Mondor, DHU Pe-Psy, hôpital A.-Chenevier, pôle de psychiatrie et d'addictologie, pavillon Hartmann, 40, rue de Mesly, 94000 Créteil, France
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Muszer M, Noszczyńska M, Kasperkiewicz K, Skurnik M. Human Microbiome: When a Friend Becomes an Enemy. Arch Immunol Ther Exp (Warsz) 2015; 63:287-98. [PMID: 25682593 PMCID: PMC4499106 DOI: 10.1007/s00005-015-0332-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/12/2014] [Indexed: 12/24/2022]
Abstract
The microorganisms that inhabit humans are very diverse on different body sites and tracts. Each specific niche contains a unique composition of the microorganisms that are important for a balanced human physiology. Microbial cells outnumber human cells by tenfold and they function as an invisible organ that is called the microbiome. Excessive use of antibiotics and unhealthy diets pose a serious danger to the composition of the microbiome. An imbalance in the microbial community may cause pathological conditions of the digestive system such as obesity, cancer and inflammatory bowel disease; of the skin such as atopic dermatitis, psoriasis and acne and of the cardiovascular system such as atherosclerosis. An unbalanced microbiome has also been associated with neurodevelopmental disorders such as autism and multiple sclerosis. While the microbiome has a strong impact on the development of the host immune system, it is suspected that it can also be the cause of certain autoimmune diseases, including diabetes or rheumatoid arthritis. Despite the enormous progress in the field, the interactions between the human body and its microbiome still remain largely unknown. A better characterization of the interactions may allow for a deeper understanding of human disease states and help to elucidate a possible association between the composition of the microbiome and certain pathologies. This review focuses on general findings that are related to the area and provides no detailed information about the case of study. The aim is to give some initial insight on the studies of the microbiome and its connection with human health.
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Affiliation(s)
- Magdalena Muszer
- Department of Microbiology, University of Silesia, Katowice, Poland
| | | | | | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
- University Central Hospital Laboratory Diagnostics, Helsinki, Finland
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Dudonné S, Varin TV, Forato Anhê F, Dubé P, Roy D, Pilon G, Marette A, Levy É, Jacquot C, Urdaci M, Desjardins Y. Modulatory effects of a cranberry extract co-supplementation with Bacillus subtilis CU1 probiotic on phenolic compounds bioavailability and gut microbiota composition in high-fat diet-fed mice. PHARMANUTRITION 2015. [DOI: 10.1016/j.phanu.2015.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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O'Neal L, Obregón-Tito AJ, Tito RY, Ozga AT, Polo SI, Lewis CM, Lawson PA. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru. Anaerobe 2015; 35:33-7. [PMID: 26123611 DOI: 10.1016/j.anaerobe.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)).
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Affiliation(s)
- Lindsey O'Neal
- Department of Microbiology and Plant Biology, University of Oklahoma, USA
| | | | - Raul Y Tito
- Department of Anthropology, University of Oklahoma, USA
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, USA
| | - Susan I Polo
- Department of Anthropology, University of Oklahoma, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, USA
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, USA.
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Freitas TAK, Li PE, Scholz MB, Chain PSG. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res 2015; 43:e69. [PMID: 25765641 PMCID: PMC4446416 DOI: 10.1093/nar/gkv180] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/17/2015] [Accepted: 02/22/2015] [Indexed: 12/23/2022] Open
Abstract
A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
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Affiliation(s)
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Matthew B Scholz
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Abstract
The human body hosts rich and diverse microbial communities. Our microbiota affects the normal human physiology, and compositional changes might alter host homeostasis and, therefore, disease risk. The microbial community structure may sometimes occupy discrete configurations and under certain circumstances vary continuously. The ability to characterize accurately the ecology of human-associated microbial communities became possible by advances in deep sequencing and bioinformatics analyses.
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Affiliation(s)
- Gidon Berger
- Department of Internal Medicine B, Rambam Health Care Campus, Haifa, Israel
| | - Roni Bitterman
- Department of Internal Medicine B, Rambam Health Care Campus, Haifa, Israel
| | - Zaher S. Azzam
- Department of Internal Medicine B, Rambam Health Care Campus, Haifa, Israel
- Ruth & Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
- To whom correspondence should be addressed. E-mail:
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Shabbir MZ, Malys T, Ivanov YV, Park J, Shabbir MAB, Rabbani M, Yaqub T, Harvill ET. Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan. Poult Sci 2015; 94:612-20. [PMID: 25667427 DOI: 10.3382/ps/pev010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Commercial poultry is an important agricultural industry worldwide. Although dense living conditions and large flocks increase meat and egg production, they also increase the risk of disease outbreaks and zoonoses. Current pathogen identification methods mostly rely on culture-dependent techniques and, therefore, are limited to a very small number of bacteria present in the environment. Next Generation Sequencing allows for culture-independent characterization of lower respiratory microbiome of birds including the identification of novel commensals and potentially emerging pathogens. In this study, we collected tracheo-bronchoalveolar lavage of 14 birds raised at 3 different farms in the Punjab province of Pakistan. To characterize the lower respiratory microbiome of these birds, we sequenced hyper-variable regions of the 16S ribosomal subunit gene. Although dominated by bacteria belonging to a small number of taxonomic classifications, the lower respiratory microbiome from each farm was far more diverse and novel than previously known. The differences in microbiome among farms suggest that inter-farm differences affect the microbiome of birds more than breed, geographic location, or management system. The presence of potential and known pathogens in genetically similar specialty breeds of chickens kept at unnaturally high densities and under variable conditions presents an extraordinary opportunity for the selection of highly pathogenic bacteria. In some instances, opportunistic respiratory pathogens were observed in apparently healthy birds. Understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats.
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Affiliation(s)
- Muhammad Zubair Shabbir
- Quality Operations Laboratory, University of Veterinary and Animal Sciences Lahore 54600, Pakistan
| | - Tyler Malys
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802
| | - Yury V Ivanov
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802
| | - Jihye Park
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802
| | | | - Masood Rabbani
- University Diagnostic Laboratory, University of Veterinary and Animal Science, Lahore 54600, Pakistan
| | - Tahir Yaqub
- Quality Operations Laboratory, University of Veterinary and Animal Sciences Lahore 54600, Pakistan
| | - Eric Thomas Harvill
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802
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Ogba OM, Abia-Bassey L. Cryptococcal antigenemia among HIV seropositive patients accessing care in antiretroviral therapy (ART) clinics in Calabar, South Southern Nigeria. ACTA ACUST UNITED AC 2015. [DOI: 10.7243/2052-6180-3-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lin M, Xie Z, Zhou Y, Li Y, Ren J, Peng XX, Yao M, Yang Z, Liao Q. Dynamic metabonomic and microbiological response of rats to lincomycin exposure: an integrated microbiology and metabonomics analysis. RSC Adv 2015. [DOI: 10.1039/c5ra10626e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We investigated the changes of gut microbiome, host metabolism and their relationships of lincomycin exposure by microbiological and metabolomics profiling.
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Affiliation(s)
- Manna Lin
- School of Chinese Materia Medica
- Guangzhou University of Chinese Medicine
- Guangzhou
- P. R. China
- School of Pharmaceutical Sciences
| | - Zhiyong Xie
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Yuting Zhou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Yemeng Li
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Jian Ren
- School of Life Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Xuan-xian Peng
- School of Life Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Meicun Yao
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Zhongzhou Yang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Qiongfeng Liao
- School of Chinese Materia Medica
- Guangzhou University of Chinese Medicine
- Guangzhou
- P. R. China
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40
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Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Assembly of viral genomes from metagenomes. Front Microbiol 2014; 5:714. [PMID: 25566226 PMCID: PMC4270193 DOI: 10.3389/fmicb.2014.00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/30/2014] [Indexed: 11/20/2022] Open
Abstract
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
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Affiliation(s)
- Saskia L. Smits
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
| | - Aritz Ruiz-Gonzalez
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA)Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine HannoverHannover, Germany
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
- Center for Infection Medicine and Zoonoses ResearchHannover, Germany
| | - Anita C. Schürch
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
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41
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Patel NB, Tito RY, Obregón-Tito AJ, O'Neal L, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Hamada M, Uchino Y, Lewis CM, Lawson PA. Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru. Anaerobe 2014; 32:43-48. [PMID: 25481562 DOI: 10.1016/j.anaerobe.2014.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/13/2022]
Abstract
A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1ω9c (39.8%), C18:2ω6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4α (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)).
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Affiliation(s)
- Nisha B Patel
- Department of Microbiology and Plant Biology, University of Oklahoma, USA
| | - Raul Y Tito
- Department of Anthropology, University of Oklahoma, USA; Universidad Cientifica del Sur, Lima, Peru
| | - Alexandra J Obregón-Tito
- Department of Anthropology, University of Oklahoma, USA; Universidad Cientifica del Sur, Lima, Peru
| | - Lindsey O'Neal
- Department of Microbiology and Plant Biology, University of Oklahoma, USA
| | | | - Luis Marin-Reyes
- Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | | | | | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yoshihito Uchino
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, USA
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, USA.
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42
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Cheng S, Karkar S, Bapteste E, Yee N, Falkowski P, Bhattacharya D. Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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43
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Lo Sasso G, Ryu D, Mouchiroud L, Fernando SC, Anderson CL, Katsyuba E, Piersigilli A, Hottiger MO, Schoonjans K, Auwerx J. Loss of Sirt1 function improves intestinal anti-bacterial defense and protects from colitis-induced colorectal cancer. PLoS One 2014; 9:e102495. [PMID: 25013930 PMCID: PMC4094521 DOI: 10.1371/journal.pone.0102495] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 06/19/2014] [Indexed: 01/09/2023] Open
Abstract
Dysfunction of Paneth and goblet cells in the intestine contributes to inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CAC). Here, we report a role for the NAD+-dependent histone deacetylase SIRT1 in the control of anti-bacterial defense. Mice with an intestinal specific Sirt1 deficiency (Sirt1int−/−) have more Paneth and goblet cells with a consequent rearrangement of the gut microbiota. From a mechanistic point of view, the effects on mouse intestinal cell maturation are mediated by SIRT1-dependent changes in the acetylation status of SPDEF, a master regulator of Paneth and goblet cells. Our results suggest that targeting SIRT1 may be of interest in the management of IBD and CAC.
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Affiliation(s)
- Giuseppe Lo Sasso
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Dongryeol Ryu
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Mouchiroud
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Samodha C. Fernando
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Christopher L. Anderson
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Elena Katsyuba
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandra Piersigilli
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Michael O. Hottiger
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Kristina Schoonjans
- Institute of Bioengineering, School of Life Science, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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44
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Cuntz U. Grundkonzepte der gastrointestinalen Psychophysiologie. VERHALTENSTHERAPIE 2014. [DOI: 10.1159/000362913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2014; 20:714-37. [PMID: 24093227 DOI: 10.1089/cmb.2013.0084] [Citation(s) in RCA: 993] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "microbial dark matter" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (cultivated monostrain) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet. Thus, recently developed single-cell assemblers not only enable single-cell sequencing, but also improve on conventional assemblers on their own turf. SPAdes is available for free online download under a GPLv2 license.
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Affiliation(s)
- Sergey Nurk
- 1 Algorithmic Biology Laboratory, St. Petersburg Academic University , Russian Academy of Sciences, St. Petersburg, Russia
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An C, Kuda T, Yazaki T, Takahashi H, Kimura B. Caecal environment of rats fed far East Asian-modelled diets. Appl Microbiol Biotechnol 2014; 98:4701-9. [DOI: 10.1007/s00253-014-5535-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 02/07/2023]
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48
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Pfefferle PI, Renz H. The mucosal microbiome in shaping health and disease. F1000PRIME REPORTS 2014; 6:11. [PMID: 24592323 PMCID: PMC3914505 DOI: 10.12703/p6-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
More than 300 years after Antonie van Leeuwenhoek gave the first description of microbes that colonize human body surfaces, the re-discovery of this multifaceted microbial world within our bodies has challenged our principal view on microbes. Novel sequencing techniques provide a plethora of (meta)genomic data, which elucidate the unique properties of mircobiota in different subjects. Moreover, the variety of metabolic and immunologic interactions between the mircobiota and the host's epithelial surfaces has challenged the paradigm of a unidirectional interplay between a given pathogen and the host's immune defense. The newly discovered mechanisms that underlie the symbiosis between the host, specific colonizers, and the mircobiota as a whole indicate that this colonization is more than a friendly coexistence. In fact, it represents a complex ecosystem with implications for the human metabolic homeostasis and immune tolerance. The resilience of the mircobiota and the capability to maintain a well-established equilibrium between symbionts and potential pathogens seem to be determining factors in shaping health or disease.
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Affiliation(s)
- Petra Ina Pfefferle
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics Philipps University Marburg, Biomedical Research CentreHans-Meerweinstr. 2, 35043 MarburgGermany
- University of Gießen and Marburg Lung Center (UGMLC), Member of the German Lung Center for Lung Research (DZL)
| | - Harald Renz
- University of Gießen and Marburg Lung Center (UGMLC), Member of the German Lung Center for Lung Research (DZL)
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH, Campus MarburgBaldingerstrasse 33, 35043 Marburg
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49
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Selective proliferation of intestinal Barnesiella under fucosyllactose supplementation in mice. Br J Nutr 2014; 111:1602-10. [PMID: 24411010 DOI: 10.1017/s0007114513004200] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The oligosaccharides 2-fucosyllactose and 3-fucosyllactose are major constituents of human breast milk but are not found in mouse milk. Milk oligosaccharides have a prebiotic action, thus affecting the colonisation of the infant intestine by microbiota. To determine the specific effect of fucosyllactose exposure on intestinal microbiota in mice, in the present study, we orally supplemented newborn mice with pure 2-fucosyllactose and 3-fucosyllactose. Exposure to 2-fucosyllactose and 3-fucosyllactose increased the levels of bacteria of the Porphyromonadaceae family in the intestinal gut, more precisely members of the genus Barnesiella as analysed by 16S pyrosequencing. The ability of Barnesiella to utilise fucosyllactose as energy source was confirmed in bacterial cultures. Whereas B. intestinihominis and B. viscericola did not grow on fucose alone, they proliferated in the presence of 2-fucosyllactose and 3-fucosyllactose following the secretion of linkage-specific fucosidase enzymes that liberated lactose. The change in the composition of intestinal microbiota mediated by fucosyllactose supplementation affected the susceptibility of mice to dextran sulphate sodium-induced colitis, as indicated by increased resistance of mice subjected to 2-fucosyllactose supplementation for 6 weeks. The present study underlines the ability of specific milk oligosaccharides to change the composition of intestinal microbiota and thereby to shape an intestinal milieu resilient to inflammatory diseases.
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50
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Sharpton TJ. An introduction to the analysis of shotgun metagenomic data. FRONTIERS IN PLANT SCIENCE 2014; 5:209. [PMID: 24982662 PMCID: PMC4059276 DOI: 10.3389/fpls.2014.00209] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/29/2014] [Indexed: 05/19/2023]
Abstract
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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Affiliation(s)
- Thomas J. Sharpton
- *Correspondence: Thomas J. Sharpton, Department of Microbiology and Department of Statistics, Oregon State University, 220 Nash Hall, Corvallis, OR 97331, USA e-mail:
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