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Liu S, Han Z, Zhu D, Luan X, Deng L, Dong L, Yang M, Zhang Y. Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil. J Environ Sci (China) 2024; 135:728-740. [PMID: 37778843 DOI: 10.1016/j.jes.2022.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 10/03/2023]
Abstract
Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liujie Deng
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Liping Dong
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Amir SE, Naeem M, Boocock D, Coveney C, O'Neill HM, Bedford MR, Burton EJ. Xylo-oligosaccharide-based prebiotics upregulate the proteins of the Sus-like system in caecal Bacteroidetes of the chicken: evidence of stimbiotic mechanism. Poult Sci 2023; 102:103113. [PMID: 37856910 PMCID: PMC10590740 DOI: 10.1016/j.psj.2023.103113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
The present study was conducted to investigate the stimbiotic mechanism of xylo-oligosaccharide (XOS) in degrading the complex polysaccharides by the caecal bacteria of the chicken, by applying a proteomic approach. A total of 800 as-hatched Ross 308 broiler chicks were equally divided into 4 experimental pens (200 chicks per pen) at a commercial poultry barn, allocating 2 pens per treatment. Birds were fed ad libitum with 2 dietary treatments; CON (without XOS) and XOS (with 0.1g XOS/kg diet) from d 0 to 35. From each pen, 60 Individual birds were weighed weekly whereas caecal content was obtained from 5 birds cervically dislocated on d 35. The caecal bacteria were lysed and their proteins were quantified using label-free quantitative proteomic mass spectrometry. The results showed that XOS significantly increased (P < 0.05) bird weight on d 7, 14, 21, and 28, and body weight gain on d 7, 14, 21, and 35 compared to CON. However, no difference (P > 0.05) in body weight gain was observed from d 0 to 35 between CON and XOS. The proteomic analysis of caecal bacteria revealed that 29 proteins were expressed differently between the CON and the XOS group. Out of 29, 20 proteins were significantly increased in the XOS group compared to CON and 9 of those proteins belonged to the starch-utilizing system (Sus)-like system of the gram-negative Bacteroidetes. Bacteroides thetaiotaomicron (Bt) is a significant constituent of the human gut microbiota, known for its remarkable ability to hydrolyze most glycosidic bonds of polysaccharides. This microorganism possesses a 5-protein complex in its outer membrane, named the starch utilization system (Sus), responsible for adhering to, breaking down, and transporting starch into the cell. Sus serves as an exemplar system for numerous polysaccharide utilization loci that target glycans found in Bt and other members of the Bacteroidetes phylum. The proteins of the Sus-like system are involved in the degradation of complex polysaccharides and transportation of the oligosaccharides into the periplasm of the caecal bacteria where they are further broken down into smaller units. These smaller units are then transported into the cytoplasm of the cell where they are utilized in metabolic pathways leading to potential generation of short-chain fatty acids, thus improving the nutritive value of residual feed. In conclusion, XOS supplementation upregulates the expression of the proteins of the Sus-like system indicating its role as a stimbiotic.
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Affiliation(s)
- Saba E Amir
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG25 0QF, United Kingdom
| | - M Naeem
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG25 0QF, United Kingdom.
| | - David Boocock
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NF, United Kingdom
| | - Clare Coveney
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NF, United Kingdom
| | - H M O'Neill
- AB Vista, Marlborough, SN8 4AN, United Kingdom
| | - M R Bedford
- AB Vista, Marlborough, SN8 4AN, United Kingdom
| | - E J Burton
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG25 0QF, United Kingdom
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3
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Miri S, Hassan H, Esmail GA, Njoku EN, Chiba M, Yousuf B, Ahmed TAE, Hincke M, Mottawea W, Hammami R. A Two Bacteriocinogenic Ligilactobacillus Strain Association Inhibits Growth, Adhesion, and Invasion of Salmonella in a Simulated Chicken Gut Environment. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10148-5. [PMID: 37646968 DOI: 10.1007/s12602-023-10148-5] [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] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
In this study, we aimed to develop a protective probiotic coculture to inhibit the growth of Salmonella enterica serovar Typhimurium in the simulated chicken gut environment. Bacterial strains were isolated from the digestive mucosa of broilers and screened in vitro against Salmonella Typhimurium ATCC 14028. A biocompatibility coculture test was performed, which identified two biocompatible strains, Ligilactobacillus salivarius UO.C109 and Ligilactobacillus saerimneri UO.C121 with high inhibitory activity against Salmonella. The cell-free supernatant (CFS) of the selected isolates exhibited dose-dependent effects, and the inhibitory agents were confirmed to be proteinaceous by enzymatic and thermal treatments. Proteome and genome analyses revealed the presence of known bacteriocins in the CFS of L. salivarius UO.C109, but unknown for L. saerimneri UO.C121. The addition of these selected probiotic candidates altered the bacterial community structure, increased the diversity of the chicken gut microbiota challenged with Salmonella, and significantly reduced the abundances of Enterobacteriaceae, Parasutterlla, Phascolarctobacterium, Enterococcus, and Megamonas. It also modulated microbiome production of short-chain fatty acids (SCFAs) with increased levels of acetic and propionic acids after 12 and 24 h of incubation compared to the microbiome challenged with S. Typhimurium. Furthermore, the selected probiotic candidates reduced the adhesion and invasion of Salmonella to Caco-2 cells by 37-39% and 51%, respectively, after 3 h of incubation, compared to the control. These results suggest that the developed coculture probiotic strains has protective activity and could be an effective strategy to control Salmonella infections in poultry.
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Affiliation(s)
- Saba Miri
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Hebatoallah Hassan
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Galal Ali Esmail
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Emmanuel N Njoku
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Mariem Chiba
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Basit Yousuf
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Tamer A E Ahmed
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
| | - Maxwell Hincke
- Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, K1H8M5, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, K1H8M5, Ottawa, ON, Canada
| | - Walid Mottawea
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Riadh Hammami
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, K1N 6N5, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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4
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Tilocca B, Soggiu A, Iavarone F, Greco V, Putignani L, Ristori MV, Macari G, Spina AA, Morittu VM, Ceniti C, Piras C, Bonizzi L, Britti D, Urbani A, Figeys D, Roncada P. The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective. Int J Mol Sci 2022; 23:ijms232214131. [PMID: 36430609 PMCID: PMC9698706 DOI: 10.3390/ijms232214131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Alessio Soggiu
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | - Maria Vittoria Ristori
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | | | - Anna Antonella Spina
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Valeria Maria Morittu
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Carlotta Ceniti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristian Piras
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Luigi Bonizzi
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Domenico Britti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Paola Roncada
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: ; Tel.: +39-096-1369-4284
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5
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Dehau T, Ducatelle R, Immerseel FV, Goossens E. Omics technologies in poultry health and productivity - part 1: current use in poultry research. Avian Pathol 2022; 51:407-417. [PMID: 35675291 DOI: 10.1080/03079457.2022.2086447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.
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Affiliation(s)
- Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Nguyen BAT, Chen QL, He JZ, Hu HW. Livestock manure spiked with the antibiotic tylosin significantly altered soil protist functional groups. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:127867. [PMID: 34844807 DOI: 10.1016/j.jhazmat.2021.127867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
With the increasing global antibiotic uses in livestock husbandry, animal manures upon land application pose potential threats to the environments and soil microbiome. Nevertheless, effects of manures and antibiotic-administered manures on soil protists, an integral component of soil food web and primary regulators of bacteria, remain unknown. Here, we assessed impacts of cattle and poultry manures with or without an antibiotic tylosin on soil protists and their functional groups in a 130-day microcosm incubation. Protists were highly responsive to manure application, with a significant decline in their alpha diversity in all manure treatments. There were also significant temporal changes in the alpha diversity and composition of soil protists and their functional groups. Poultry manures had stronger negative influences on the community structure of protists compared to cattle manures, and more pronounced effects on protists were observed in tylosin-spiked manure treatments. Furthermore, many consumer, phototrophic and parasitic taxa were highly susceptible to all manure treatments at Day 50 and 130. Altogether, our findings demonstrate negative effects of animal manures and tylosin on soil protists. This study suggests that the applications of livestock manures and antibiotics may subsequently alter ecological functions of protists and their interactions with other soil microorganisms in agricultural systems.
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Affiliation(s)
- Bao-Anh T Nguyen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Qing-Lin Chen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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7
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Dittoe DK, Olson EG, Ricke SC. IMPACT OF THE GASTROINTESTINAL MICROBIOME AND FERMENTATION METABOLITES ON BROILER PERFORMANCE. Poult Sci 2022; 101:101786. [PMID: 35346496 PMCID: PMC9079343 DOI: 10.1016/j.psj.2022.101786] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dana K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Elena G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA.
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8
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Xing SC, Huang CB, Wu RT, Yang YW, Chen JY, Mi JD, Wu YB, Wang Y, Liao XD. Breed differences in the expression levels of gga-miR-222a in laying hens influenced H 2S production by regulating methionine synthase genes in gut bacteria. MICROBIOME 2021; 9:177. [PMID: 34433492 PMCID: PMC8390279 DOI: 10.1186/s40168-021-01098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/20/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The microbiota in the cecum of laying hens is crucial for host digestion, metabolism, and odor gas production. The results of recent studies have suggested that host microRNAs (miRNAs) can regulate gene expression of the gut microbiota. In the present study, the expression profiles of host-derived miRNAs in the cecal content of two laying hen breeds; Hy-line Gray and Lohmann Pink, which have dissimilar H2S production, were characterized; and their effects on H2S production by regulating the expression of gut microbiota-associated genes were demonstrated. RESULTS The differential expression of microbial serine O-acetyltransferase, methionine synthase, aspartate aminotransferase, methionine-gamma-lyase, and adenylylsulfate kinase between the two hen breeds resulted in lower H2S production in the Hy-line hens. The results also revealed the presence of miRNA exosomes in the cecal content of laying hens, and an analysis of potential miRNA-target relationships between 9 differentially expressed miRNAs and 9 differentially expressed microbial genes related to H2S production identified two methionine synthase genes, Odosp_3416 and BF9343_2953, that are targeted by gga-miR-222a. Interestingly, in vitro fermentation results showed that gga-miR-222a upregulates the expression of these genes, which increased methionine concentrations but decreased H2S production and soluble sulfide concentrations, indicating the potential of host-derived gga-miR-222a to reduce H2S emission in laying hens. CONCLUSION The findings of the present study reveal both a physiological role by which miRNAs shape the cecal microbiota of laying hens and a strategy to use host miRNAs to manipulate the microbiome and actively express key microbial genes to reduce H2S emissions and breed environmentally friendly laying hens. Video Abstract.
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Affiliation(s)
- Si-Cheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642 Guangdong China
- National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642 Guangdong China
| | - Chun-Bo Huang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Rui-Ting Wu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Yi-Wen Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Jing-Yuan Chen
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Jian-Dui Mi
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642 Guangdong China
- National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642 Guangdong China
| | - Yin-Bao Wu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642 Guangdong China
- National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642 Guangdong China
| | - Yan Wang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642 Guangdong China
- National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642 Guangdong China
| | - Xin-Di Liao
- College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642 Guangdong China
- National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642 Guangdong China
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9
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Shiraishi Y, Kryukov K, Tomomatsu K, Sakamaki F, Inoue S, Nakagawa S, Imanishi T, Asano K. Diagnosis of pleural empyema/parapneumonic effusion by next-generation sequencing. Infect Dis (Lond) 2021; 53:450-459. [PMID: 33689538 DOI: 10.1080/23744235.2021.1892178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Although a microbiological diagnosis of pleural infection is clinically important, it is often complicated by prior antibiotic treatment and/or difficulties with culturing some bacterial species. Therefore, we aimed to identify probable causative bacteria in pleural empyema/parapneumonic effusions by combining 16S ribosomal RNA (rRNA) gene amplification and next-generation sequencing (NGS). METHODS Pleural fluids were collected from 19 patients with infectious effusions and nine patients with non-infectious malignant effusions. We analysed DNA extracted from the pleural fluid supernatant by NGS using the Genome Search Toolkit and GenomeSync database, either directly or after PCR amplification of the 16S rRNA gene. Infectious and non-infectious effusions were distinguished by semi-quantitative PCR of the 16S rRNA gene. RESULTS Only 8 (42%) effusions were culture-positive, however, NGS of the 16S rRNA gene amplicon identified 14 anaerobes and 7 aerobes/facultative anaerobes in all patients, including Streptococcus sp. (n = 6), Fusobacterium sp. (n = 5), Porphyromonas sp. (n = 5), and Prevotella sp. (n = 4), accounting for >10% of the total genomes. The culture and NGS results were discordant for 3 out of 8 patients, all of whom had previously been treated with antibiotics. Total (2ΔCT value in semi-quantitative PCR of the 16S rRNA gene) and specific (total bacterial load multiplied by the proportion of primary bacteria in NGS) bacterial loads could efficiently distinguish empyema/parapneumonic effusion from non-infectious effusion. CONCLUSION Combining NGS with semi-quantitative PCR can facilitate the diagnosis of pleural empyema/parapneumonic effusion and its causal bacteria.
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Affiliation(s)
- Yoshiki Shiraishi
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.,Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Katsuyoshi Tomomatsu
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Fumio Sakamaki
- Division of Respiratory Disease, Department of Medicine, Tokai University Hachioji Hospital, Tokyo, Japan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Koichiro Asano
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
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10
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Cui L, Zhang X, Cheng R, Ansari AR, Elokil AA, Hu Y, Chen Y, Nafady AA, Liu H. Sex differences in growth performance are related to cecal microbiota in chicken. Microb Pathog 2020; 150:104710. [PMID: 33383151 DOI: 10.1016/j.micpath.2020.104710] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/05/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
In poultry industry, male chickens have a better growth performance than female ones under the same genetic background and diet. Emerging evidences proposed an important role of intestinal microbiota in chicken's growth performance. This study aimed to determine gut microbiota related gender based differences in the growth performance of chickens. Therefore, male and female chickens (n = 20) at 7-week age were used to carry out histomorphological, molecular, gene expression analysis with their liver, chest and leg muscle, as well as 16S rRNA sequencing analysis for gut microbiota. The results revealed that Bacteroides and Megamonas genera were more prominently colonized in the cecum of male chickens. The male chicken's cecal microbiota indicated a closer relation with glycan metabolism, while in the female chickens it was more related with lipid metabolism. Gene expression levels associated with glycan and lipid metabolism were different between male and female chickens. Further, using Spearman correlation analysis, we found a positive correlation between glycan and lipid metabolism, and the relative abundance of Bacteroides, Megamona and Lactobacillus in male chickens. Similarly, we also found a positive correlation between the lipid metabolism and the relative abundance of Ruminococcaceae and Enterococcus in female chickens. These findings revealed the association of chicken growth performance with cecal microbiota that contributed to the metabolism of glycan and lipid in a sex-dependent manner.
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Affiliation(s)
- Lei Cui
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolong Zhang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ranran Cheng
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Abdur Rahman Ansari
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Section of Anatomy and Histology, Department of Basic Sciences, College of Veterinary and Animal Sciences (CVAS) Jhang; University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - Abdelmotaleb A Elokil
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor, 13736, Egypt
| | - Yafang Hu
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Chen
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Abdallah A Nafady
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huazhen Liu
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Lee SJ, Cho S, La TM, Lee HJ, Lee JB, Park SY, Song CS, Choi IS, Lee SW. Comparison of microbiota in the cloaca, colon, and magnum of layer chicken. PLoS One 2020; 15:e0237108. [PMID: 32750076 PMCID: PMC7402502 DOI: 10.1371/journal.pone.0237108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022] Open
Abstract
Anatomically terminal parts of the urinary, reproductive, and digestive systems of birds all connect to the cloaca. As the feces drain through the cloaca in chickens, the cloacal bacteria were previously believed to represent those of the digestive system. To investigate similarities between the cloacal microbiota and the microbiota of the digestive and reproductive systems, microbiota inhabiting the colon, cloaca, and magnum, which is a portion of the chicken oviduct of 34-week-old, specific-pathogen-free hens were analyzed using a 16S rRNA metagenomic approach using the Ion torrent sequencer and the Qiime2 bioinformatics platform. Beta diversity via unweighted and weighted unifrac analyses revealed that the cloacal microbiota was significantly different from those in the colon and the magnum. Unweighted unifrac revealed that the cloacal microbiota was distal from the microbiota in the colon than from the microbiota in the magnum, whereas weighted unifrac revealed that the cloacal microbiota was located further away from the microbiota in the magnum than from the microbiota inhabiting the colon. Pseudomonas spp. were the most abundant in the cloaca, whereas Lactobacillus spp. and Flavobacterium spp. were the most abundant species in the colon and the magnum. The present results indicate that the cloaca contains a mixed population of bacteria, derived from the reproductive, urinary, and digestive systems, particularly in egg-laying hens. Therefore, sampling cloaca to study bacterial populations that inhabit the digestive system of chickens requires caution especially when applied to egg-laying hens. To further understand the physiological role of the microbiota in chicken cloaca, exploratory studies of the chicken’s cloacal microbiota should be performed using chickens of different ages and types.
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Affiliation(s)
- Seo-Jin Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Seongwoo Cho
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Tae-Min La
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hong-Jae Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Joong-Bok Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Seung-Yong Park
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - In-Soo Choi
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Sang-Won Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- * E-mail:
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12
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Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes 2020; 6:23. [PMID: 32504001 PMCID: PMC7275042 DOI: 10.1038/s41522-020-0133-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.
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13
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Dong X, Rao D, Tian L, Wang Q, Yang K. A slurry microcosm study on the interaction between antibiotics and soil bacterial community. Heliyon 2020; 6:e03348. [PMID: 32055738 PMCID: PMC7005453 DOI: 10.1016/j.heliyon.2020.e03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/09/2019] [Accepted: 01/30/2020] [Indexed: 12/26/2022] Open
Abstract
Antibiotics released in the environment have attracted great attention. The environmental emission control of antibiotics should be based on the degree of their negative impacts on the environment and ecology. Here, we conducted a series of soil slurry microcosm experiments to investigate the interactions between antibiotics and the soil bacterial community. In the soil slurry, distinctive behaviors were observed for different antibiotics. Beta-lactams (ampicillin and ceftriaxone) experienced fast biodegradation. Kanamycin was adsorbed on soil particles soon after its addition. Nalidixic acid was stable throughout the experimental period (164 h). The main inactivation mechanism of tetracycline was deduced to be hydrolysis. Bacterial communities in slurries with or without antibiotic-treatment were profiled via high-throughput Illumina sequencing of the 16S rRNA gene. Unstable (ceftriaxone) and adsorbed (kanamycin) antibiotics show minor or negligible influences on the soil bacterial community. Stable antibiotics (nalidixic acid and tetracycline) have significantly affected the structure of the bacterial community. Most of enriched bacterial genera by various antibiotics belong to the same phylum, Proteobacteria. Inhibited bacterial phyla by nalidixic acid are Firmicutes and Bacteroidetes, while those inhibited by tetracycline are Firmicutes, Bacteroidetes and Cyanobacteria. According to the PICRUSt prediction of metagenome, influence of antibiotics on overall metabolic function of the bacterial community is rather limited. This study has provided valuable information, from a phylogenetic viewpoint, about the influence of high concentration of antibiotics on soil bacterial community.
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Affiliation(s)
- Xiaohong Dong
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Dawei Rao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Lejin Tian
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Qizheng Wang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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14
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Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome. PLoS One 2020; 15:e0228338. [PMID: 31978143 PMCID: PMC6980619 DOI: 10.1371/journal.pone.0228338] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
In this study we gained insights into the effects of the supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) in the chicken drinking water on crop and caeca microbiomes. The probiotic was supplemented at the concentrations of 0.2 g Lactobacillus acidophilus/day/bird and 0.02 g Lactobacillus acidophilus/day/bird and its effect on the crop and caeca microbiomes was assessed at 14 and 35 days of rearing. The results showed that mean relative abundance of Lactobacillus acidophilus in the caeca did not show significative differences in the treated and control birds, although Lactobacillus acidophilus as well as Faecalibacterium prausnitzii, Lactobacillus crispatus and Lactobacillus reuteri significantly increased over time. Moreover, the treatment with the high dose of probiotic significantly increased the abundance of Clostridium asparagiforme, Clostridium hathewayi and Clostridium saccharolyticum producing butyrate and other organic acids supporting the chicken health. Finally, at 35 days, the Cell division protein FtsH (EC 3.4.24.-) and the Site-specific recombinase genes were significantly increased in the caeca of birds treated with the high dose of probiotic in comparison to the control group. The results of this study showed that Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in the drinking water at the concentrations of 0.2 and 0.02 g Lactobacillus acidophilus/day/bird improved beneficial microbes and functional genes in broiler crops and caeca. Nevertheless, the main site of action of the probiotic is the crop, at least in the early stage of the chicken life. Indeed, at 14 days Lactobacillus acidophilus was significantly higher in the crops of chickens treated with the high dose of LA in comparison to the control (14.094 vs 1.741%, p = 0.036).
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15
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Metatranscriptomics and Metaproteomics for Microbial Communities Profiling. UNRAVELLING THE SOIL MICROBIOME 2020. [DOI: 10.1007/978-3-030-15516-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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16
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Peters DL, Wang W, Zhang X, Ning Z, Mayne J, Figeys D. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome. Proteomics 2019; 19:e1800363. [PMID: 31321880 DOI: 10.1002/pmic.201800363] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.
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Affiliation(s)
- Danielle L Peters
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Wenju Wang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada.,Canadian Institute for Advanced Research, 661 University Ave, Toronto, ON, M5G 1M1, Canada.,The University of Ottawa and Shanghai Institute of Materia Medica Joint Research Center on Systems and Personalized Pharmacology, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
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17
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Queirós J, Villar M, Hernández-Jarguín A, López V, Fernández de Mera I, Vicente J, Alves PC, Gortazar C, Fuente JDL. A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection. Tuberculosis (Edinb) 2018; 114:103-112. [PMID: 30711148 DOI: 10.1016/j.tube.2018.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/14/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022]
Abstract
Constraints in the characterization of microbiota community that circulates in the host have limited the extent of co-infection studies in natural populations. In this study, we used a metaproteomics approach to characterize the mandibular lymph nodes microbiota of wild boar (Sus scrofa) naturally exposed to an increasing trend of Mycobacterium tuberculosis complex (MTC) infection. Our results showed a reduction in microbiota diversity and changes in the composition, structure and functionality of the microbiota community associated with an increase in tuberculosis prevalence, from 45% in 2002/06 to 83% in 2009/12. These temporal changes were accompanied by an increase in the relative abundance of Babesia, Theileria and Pestivirus genera and a decrease in the Ascogregarina and Chlorella. A positive association was also evidenced between the prevalence of tuberculosis and the presence of microbial proteins responsible for carbohydrate transport and metabolism. Our findings suggest MTC-host-microbiota interactions at the population level, which may occur in order to ensure sufficient metabolic resources for MTC survival, growth and transmission. We strongly recommend the use of metaproteomics when studying microbiota communities in wildlife populations, for which traditional diagnostic techniques are limited and in which new organisms with a pathogenic potential for domestic animals and humans may appear.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal; SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Angélica Hernández-Jarguín
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Vladimir López
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Isabel Fernández de Mera
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Joaquín Vicente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Paulo C Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA.
| | - Christian Gortazar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
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18
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Gielbert A, Thorne JK, Plater JM, Thorne L, Griffiths PC, Simmons MM, Cassar CA. Molecular characterisation of atypical BSE prions by mass spectrometry and changes following transmission to sheep and transgenic mouse models. PLoS One 2018; 13:e0206505. [PMID: 30408075 PMCID: PMC6224059 DOI: 10.1371/journal.pone.0206505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/14/2018] [Indexed: 11/18/2022] Open
Abstract
The prion hypothesis proposes a causal relationship between the misfolded prion protein (PrPSc) molecular entity and the disease transmissible spongiform encephalopathy (TSE). Variations in the conformation of PrPSc are associated with different forms of TSE and different risks to animal and human health. Since the discovery of atypical forms of bovine spongiform encephalopathy (BSE) in 2003, scientists have progressed the molecular characterisation of the associated PrPSc in order to better understand these risks, both in cattle as the natural host and following experimental transmission to other species. Here we report the development of a mass spectrometry based assay for molecular characterisation of bovine proteinase K (PK) treated PrPSc (PrPres) by quantitative identification of its N-terminal amino acid profiles (N-TAAPs) and tryptic peptides. We have applied the assay to classical, H-type and L-type BSE prions purified from cattle, transgenic (Tg) mice expressing the bovine (Tg110 and Tg1896) or ovine (TgEM16) prion protein gene, and sheep brain. We determined that, for classical BSE in cattle, the G96 N-terminal cleavage site dominated, while the range of cleavage sites was wider following transmission to Tg mice and sheep. For L-BSE in cattle and Tg bovinised mice, a C-terminal shift was identified in the N-TAAP distribution compared to classical BSE, consistent with observations by Western blot (WB). For L-BSE transmitted to sheep, both N-TAAP and tryptic peptide profiles were found to be changed compared to cattle, but less so following transmission to Tg ovinised mice. Relative abundances of aglycosyl peptides were found to be significantly different between the atypical BSE forms in cattle as well as in other hosts. The enhanced resolution provided by molecular analysis of PrPres using mass spectrometry has improved insight into the molecular changes following transmission of atypical BSE to other species.
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Affiliation(s)
- Adriana Gielbert
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
- * E-mail:
| | - Jemma K. Thorne
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Jane M. Plater
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Leigh Thorne
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Peter C. Griffiths
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Marion M. Simmons
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
| | - Claire A. Cassar
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, United Kingdom
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19
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Shang Y, Kumar S, Oakley B, Kim WK. Chicken Gut Microbiota: Importance and Detection Technology. Front Vet Sci 2018; 5:254. [PMID: 30406117 PMCID: PMC6206279 DOI: 10.3389/fvets.2018.00254] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 12/29/2022] Open
Abstract
Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.
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Affiliation(s)
- Yue Shang
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Sanjay Kumar
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Brian Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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20
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Wang AY, Thuy-Boun PS, Stupp GS, Su AI, Wolan DW. Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass. J Proteome Res 2018; 17:2978-2986. [PMID: 30019906 DOI: 10.1021/acs.jproteome.8b00166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram- and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble postlysis fractions differ significantly. Additionally, in the case of Gram- Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.
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Affiliation(s)
- Ana Y Wang
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Peter S Thuy-Boun
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Gregory S Stupp
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Andrew I Su
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dennis W Wolan
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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21
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Xiao Y, Xiang Y, Zhou W, Chen J, Li K, Yang H. Microbial community mapping in intestinal tract of broiler chicken. Poult Sci 2018; 96:1387-1393. [PMID: 28339527 DOI: 10.3382/ps/pew372] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/02/2016] [Indexed: 01/05/2023] Open
Abstract
Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.
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Affiliation(s)
- Yingping Xiao
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yun Xiang
- Animal Husbandry and Veterinary Institute, Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Weidong Zhou
- Animal Husbandry and Veterinary Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jinggang Chen
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaifeng Li
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Borda-Molina D, Seifert J, Camarinha-Silva A. Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome. Comput Struct Biotechnol J 2018; 16:131-139. [PMID: 30026889 PMCID: PMC6047366 DOI: 10.1016/j.csbj.2018.03.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 12/29/2022] Open
Abstract
The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics. However, the respective analyses are still at the beginning and currently there is a lack of information in regard to the activity and functional characterization of the gut microbial communities. In the future, the use of multi-omics approaches may enhance research related to chicken production, animal and also public health. Furthermore, combinations with other disciplines such as genomics, immunology and physiology may have the potential to elucidate the definition of a "healthy" gut microbiota.
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Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, Li A, Zeng Z, Zhang T. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. MICROBIOME 2018; 6:34. [PMID: 29439741 PMCID: PMC5811963 DOI: 10.1186/s40168-018-0419-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qinglin Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Andong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Tomonaga S, Okuyama H, Tachibana T, Makino R. Effects of high ambient temperature on plasma metabolomic profiles in chicks. Anim Sci J 2017; 89:448-455. [DOI: 10.1111/asj.12951] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/04/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Shozo Tomonaga
- Division of Applied Biosciences; Graduate School of Agriculture; Kyoto University; Kyoto Japan
| | - Hirofumi Okuyama
- Department of Agrobiological Science; Faculty of Agriculture; Ehime University; Matsuyama Japan
| | - Tetsuya Tachibana
- Department of Agrobiological Science; Faculty of Agriculture; Ehime University; Matsuyama Japan
| | - Ryosuke Makino
- Department of Agrobiological Science; Faculty of Agriculture; Ehime University; Matsuyama Japan
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Tang Y, Cawthraw S, Bagnall MC, Gielbert AJ, Woodward MJ, Petrovska L. Identification of temperature regulated factors of Campylobacter jejuni and their potential roles in virulence. AIMS Microbiol 2017; 3:885-898. [PMID: 31294195 PMCID: PMC6604965 DOI: 10.3934/microbiol.2017.4.885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/24/2017] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni is the major cause of bacterial gastroenteritis in man, while it is generally regarded as a commensal of the avian gut. Consumption and handling of contaminated poultry meat products are major risk factors for human infection. The body temperature in man (37 °C) and chickens (42 °C) differ markedly, and differential gene regulation and protein expression at different temperatures may in part explain the behaviour in the two hosts. We performed proteomics analyses with C. jejuni cells grown at 37 °C and 42 °C. Time-of-flight mass spectrometry (Q-Tof) analysis was carried out after samples were digested with the Filter-Aided Sample Preparation (FASP) method and peptides were fractionated by strong anion exchanges. Differentially regulated proteins were identified by Mascot and Scaffold analyses. Triple quadrupole (QQQ) mass spectrometer analysis confirmed that a total of 33 proteins were differentially regulated between 37 °C and 42 °C. Several upregulated proteins were selected for their corresponding gene knock-out mutants to be tested for their virulence in the Galleria mellonella model. To correlate with other tissue/animal models, the GADH mutant was selected for its reduced ability to colonize chickens. At 37 °C, the mutants of outer membrane protein Omp50 and Chaperone GroEL significantly increased virulence; while at 42 °C, the mutants of YceI, Omp50, and GADH reduced virulence against Galleria mellonella compared with the wild type strains. The results of current and previous studies indicate that GADH is a virulent factor in G. mellonella and a colonization factor in chickens. The workflow of this study may prove a new way to identify stress related virulent factors. The implications of these findings are discussed for pathogenesis in the model and other hosts.
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Affiliation(s)
- Yue Tang
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Mary C Bagnall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Adriana J Gielbert
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Martin J Woodward
- Food and Nutritional Sciences, University of Reading, Whiteknights, Reading RG6 6AP, UK
| | - Liljana Petrovska
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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26
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Tilocca B, Burbach K, Heyer CME, Hoelzle LE, Mosenthin R, Stefanski V, Camarinha-Silva A, Seifert J. Dietary changes in nutritional studies shape the structural and functional composition of the pigs' fecal microbiome-from days to weeks. MICROBIOME 2017; 5:144. [PMID: 29078812 PMCID: PMC5659009 DOI: 10.1186/s40168-017-0362-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/17/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The possible impact of changes in diet composition on the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if a few days are enough to reflect the microbial response to the diet by changing the community composition and function. The present study investigated the fecal microbiome of pigs during a time span of 4 weeks after a dietary change to obtain insights regarding the time required for adaptation. Four different diets were used differing in either protein source (field peas meal vs. soybean meal) or the concentration of calcium and phosphorus (CaP). RESULTS Twelve pigs were sampled at seven time points within 4 weeks after the dietary change. Fecal samples were used to sequence the 16S rRNA gene amplicons to analyse microbial proteins via LC-MS/MS and to determine the SCFA production. The analysis of OTU abundances and quantification values of proteins showed a significant separation of three periods of time (p = 0.001). Samples from the first day are used to define the 'zero period'; samples of weeks 1 and 2 are combined as 'metabolic period' and an 'equilibrium period was defined based on samples from weeks 3 and 4. Only in this last period, a separation according to the supplementation of CaP was significantly detectable (p = 0.001). No changes were found based on the corn-soybean meal or corn-field peas administration. The analysis of possible factors causing this significant separation showed only an overall change of bacterial members and functional properties. The metaproteomic approach yielded a total of about 9700 proteins, which were used to deduce possible metabolic functions of the bacterial community. CONCLUSIONS A gradual taxonomic and functional rearrangement of the bacterial community has been depicted after a change of diet composition. The adaptation lasts several weeks despite the usually assumed time span of several days. The obtained knowledge is of a great importance for the design of future nutritional studies. Moreover, considering the high similarities between the porcine and human gastrointestinal tract anatomy and physiology, the findings of the current study might imply in the design of human-related nutritional studies.
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Affiliation(s)
- Bruno Tilocca
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Katharina Burbach
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Charlotte M. E. Heyer
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Ludwig E. Hoelzle
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Rainer Mosenthin
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Volker Stefanski
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
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Li J, Hao H, Cheng G, Liu C, Ahmed S, Shabbir MAB, Hussain HI, Dai M, Yuan Z. Microbial Shifts in the Intestinal Microbiota of Salmonella Infected Chickens in Response to Enrofloxacin. Front Microbiol 2017; 8:1711. [PMID: 28943868 PMCID: PMC5596078 DOI: 10.3389/fmicb.2017.01711] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/24/2017] [Indexed: 12/18/2022] Open
Abstract
Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method. The average values of diversity indices were higher in the control group than in the three medicated groups. Non-metric multidimensional scaling (NMDS) analysis results showed that the microbial community of high dosage group was clearly separated from the other three groups. In total, 25 genera were significantly enriched (including 6 abundant genera: Lactococcus, Bacillus, Burkholderia, Pseudomonas, Rhizobium, and Acinetobacter) and 23 genera were significantly reduced in the medicated groups than in the control group for the treatment period, but these bacterial taxa recovered to normal levels after therapy withdrawal. Additionally, 5 genera were significantly reduced in both treatment and withdrawal periods (e.g., Blautia and Anaerotruncus) and 23 genera (e.g., Enterobacter and Clostridium) were significantly decreased only in the withdrawal period, indicating that these genera might be the potential targets for the fluoroquinolones antimicrobial effects. Specially, Enterococcus was significantly reduced under high dosage of enrofloxacin treatment, while significantly enriched in the withdrawal period, which was presumably due to the resistance selection. Predicted microbial functions associated with genetic information processing were significantly decreased in the high dosage group. Overall, enrofloxacin at a dosage of 100 mg/kg b.w. significantly altered the microbial community membership and structure, and microbial functions in the chicken intestine during the medication. This study fully investigates the chicken intestinal microbiota in response to enrofloxacin treatment and identifies potential targets against which the fluoroquinolones may have potent antimicrobial effects. These results provide insights into the effects of the usage of enrofloxacin on chicken and will aid in the prudent and rational use of antibiotics in poultry industry.
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Affiliation(s)
- Jun Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Chunbei Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China
| | - Saeed Ahmed
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China
| | - Muhammad A B Shabbir
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China
| | - Hafiz I Hussain
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China
| | - Menghong Dai
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China.,MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
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29
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Kathera C, Dulla EL, Chinahadri VP, Ramesh TSM, Basavaraju S, Jasti P. Proteomic characterization and bio-informatic analysis of differentially expressed E. coli Nissle 1917 proteins with response to cocoti wine stress. 3 Biotech 2017; 7:151. [PMID: 28597165 DOI: 10.1007/s13205-017-0787-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/21/2017] [Indexed: 10/19/2022] Open
Abstract
The present study emphases the comparative proteomic analysis of Escherichia coli Nissle 1917 under cocoti palm wine stress and identified differentially expressed proteins. Protein samples were analyzed by 2-D, MALDI-TOF combined with MS access. In 2-D electrophoresis, eight differentially expressed proteins were identified: five up-regulated, two down-regulated and one newly expressed protein. Protein spots were digested with trypsin for MALDI-TOF-MS analysis; protein sequences were obtained from MASCOT search. Sequences were aligned with template using Swiss Model server. Phyre-2 was used to predict homology modeling, RasMol was used to analyze the modeling structures, PSVS server was utilized to validate the protein structure by Ramachandran's plot analysis, physical and chemical properties were analyzed using ProtParam server, Phylogenetic tree was constructed by Mega4. UniProt search helps to find protein functional information of differentially expressed proteins, involved in catalytic activities, regulation mechanisms, DNA damage stimulus, anti-termination and termination process, protein binding, electron transport mechanism, and cell signaling process functions. A detailed exploration of the proteins under cocoti palm wine stress have provided the composition, structure and functions of the expressed proteins for further investigation.
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30
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Xiao M, Yang J, Feng Y, Zhu Y, Chai X, Wang Y. Metaproteomic strategies and applications for gut microbial research. Appl Microbiol Biotechnol 2017; 101:3077-3088. [PMID: 28293710 DOI: 10.1007/s00253-017-8215-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 01/16/2023]
Abstract
The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.
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Affiliation(s)
- Mingming Xiao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Junjun Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuxin Feng
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Xin Chai
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China. .,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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De Angelis M, Calasso M, Cavallo N, Di Cagno R, Gobbetti M. Functional proteomics within the genus Lactobacillus. Proteomics 2016; 16:946-62. [PMID: 27001126 DOI: 10.1002/pmic.201500117] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 11/24/2015] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
Abstract
Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains.
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Affiliation(s)
- Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Maria Calasso
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Noemi Cavallo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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Tilocca B, Witzig M, Rodehutscord M, Seifert J. Variations of Phosphorous Accessibility Causing Changes in Microbiome Functions in the Gastrointestinal Tract of Chickens. PLoS One 2016; 11:e0164735. [PMID: 27760159 PMCID: PMC5070839 DOI: 10.1371/journal.pone.0164735] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022] Open
Abstract
The chicken gastrointestinal tract (GIT) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. For the first time, the present study analysed dietary effects on the protein inventory of the microbiome in crop and ceca of broilers. We performed quantitative label-free metaproteomics by using 1-D-gel electrophoresis coupled with LC-MS/MS to identify the structural and functional changes triggered by diets supplied with varying amount of mineral phosphorous (P) and microbial phytase (MP). Phylogenetic assessment based on label-free quantification (LFQ) values of the proteins identified Lactobacillaceae as the major family in the crop section regardless of the diet, whereas proteins belonging to the family Veillonellaceae increased with the P supplementation. Within the ceca section, proteins of Bacteroidaceae were more abundant in the P-supplied diets, whereas proteins of Eubacteriaceae decreased with the P-addition. Proteins of the Ruminococcaceae increased with the amount of MP while proteins of Lactobacillaceae were more abundant in the MP-lacking diets. Classification of the identified proteins indicated a thriving microbial community in the case of P and MP supplementation, and stressed microbial community when no P and MP were supplied. Data are available via ProteomeXchange with identifier PXD003805.
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Affiliation(s)
- Bruno Tilocca
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Maren Witzig
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- * E-mail:
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Franco Cairo JPL, Carazzolle MF, Leonardo FC, Mofatto LS, Brenelli LB, Gonçalves TA, Uchima CA, Domingues RR, Alvarez TM, Tramontina R, Vidal RO, Costa FF, Costa-Leonardo AM, Paes Leme AF, Pereira GAG, Squina FM. Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi. Front Microbiol 2016; 7:1518. [PMID: 27790186 PMCID: PMC5061848 DOI: 10.3389/fmicb.2016.01518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes). Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD) were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi. Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9) and beta-glucosidases (GH1) were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7) and endo-glucanases (GH5 and GH45), as well as classical xylanases (GH10 and GH11), were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi. Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs), which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.
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Affiliation(s)
- João P L Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Flávia C Leonardo
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Luciana S Mofatto
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Lívia B Brenelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Thiago A Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Cristiane A Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Romênia R Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Robson Tramontina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fernando F Costa
- Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Ana M Costa-Leonardo
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP) Rio Claro, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Gonçalo A G Pereira
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
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Yang Y, Deng Y, Cao L. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas. Sci Rep 2016; 6:32655. [PMID: 27600170 PMCID: PMC5013396 DOI: 10.1038/srep32655] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/12/2016] [Indexed: 02/07/2023] Open
Abstract
Microorganisms in vertebrate guts have been recognized as important symbionts influencing host life. However, it remains unclear about the gut microbiota in long-distance migratory Anseriformes herbivores, which could be functionally important for these wetland-dependent animals. We collected faeces of the greater white-fronted goose (GWFG), bean goose (BG) and swan goose (SG) from Shengjin Lake (SJL) and Poyang Lake (PYL) in the Yangtze River Floodplain, China. High-throughput sequencing of 16S rRNA V4 region was employed to depict the composition and structure of geese gut microbiota during wintering period. The dominant bacterial phyla across all samples were Firmicutes, Proteobacteria and Actinobacteria, but significant variations were detected among different goose species and sampling sites, in terms of α diversity, community structures and microbial interactions. We found a significant correlation between diet and the microbial community structure in GWFG-SJL samples. These results demonstrated that host species and diet are potential drivers of goose gut microbiota assemblies. Despite these variations, functions of geese gut microbiota were similar, with great abundances of potential genes involved in nutrient metabolism. This preliminary study would be valuable for future, exhaustive investigations of geese gut microbiota and their interactions with host.
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Affiliation(s)
- Yuzhan Yang
- School of Life Sciences, University of Science and Technology of China, Huangshan Road, Hefei, 230026, China
| | - Ye Deng
- Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lei Cao
- Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Armengaud J. Next-generation proteomics faces new challenges in environmental biotechnology. Curr Opin Biotechnol 2016; 38:174-82. [DOI: 10.1016/j.copbio.2016.02.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Polansky O, Sekelova Z, Faldynova M, Sebkova A, Sisak F, Rychlik I. Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota. Appl Environ Microbiol 2015. [PMID: 26712550 DOI: 10.1128/aem.03473-15.editor] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
The gut microbiota plays important roles in its host. However, how each microbiota member contributes to the behavior of the whole population is not known. In this study, we therefore determined protein expression in the cecal microbiota in chickens of selected ages and in 7-day-old chickens inoculated with different cecal extracts on the day of hatching. Campylobacter, Helicobacter, Mucispirillum, and Megamonas overgrew in the ceca of 7-day-old chickens inoculated with cecal extracts from donor hens. Firmicutes were characterized by ABC and phosphotransferase system (PTS) transporters, extensive acyl coenzyme A (acyl-CoA) metabolism, and expression of l-fucose isomerase. Anaerostipes, Anaerotruncus, Pseudoflavonifractor, Dorea, Blautia, and Subdoligranulum expressed spore proteins. Firmicutes (Faecalibacterium, Butyrivibrio, Megasphaera, Subdoligranulum, Oscillibacter, Anaerostipes, and Anaerotruncus) expressed enzymes required for butyrate production. Megamonas, Phascolarctobacterium, and Blautia (exceptions from the phylum Firmicutes) and all Bacteroidetes expressed enzymes for propionate production pathways. Representatives of Bacteroidetes also expressed xylose isomerase, enzymes required for polysaccharide degradation, and ExbBD, TonB, and outer membrane receptors likely to be involved in oligosaccharide transport. Based on our data, Anaerostipes, Anaerotruncus, and Subdoligranulum might be optimal probiotic strains, since these represent spore-forming butyrate producers. However, certain care should be taken during microbiota transplantation because the microbiota may behave differently in the intestinal tract of a recipient depending on how well the existing communities are established.
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Affiliation(s)
- Ondrej Polansky
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
| | - Zuzana Sekelova
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
| | - Marcela Faldynova
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
| | - Alena Sebkova
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
| | - Frantisek Sisak
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech RepublicINRS-Institut Armand-Frappier
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Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota. Appl Environ Microbiol 2015; 82:1569-76. [PMID: 26712550 DOI: 10.1128/aem.03473-15] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/19/2015] [Indexed: 12/26/2022] Open
Abstract
The gut microbiota plays important roles in its host. However, how each microbiota member contributes to the behavior of the whole population is not known. In this study, we therefore determined protein expression in the cecal microbiota in chickens of selected ages and in 7-day-old chickens inoculated with different cecal extracts on the day of hatching. Campylobacter, Helicobacter, Mucispirillum, and Megamonas overgrew in the ceca of 7-day-old chickens inoculated with cecal extracts from donor hens. Firmicutes were characterized by ABC and phosphotransferase system (PTS) transporters, extensive acyl coenzyme A (acyl-CoA) metabolism, and expression of l-fucose isomerase. Anaerostipes, Anaerotruncus, Pseudoflavonifractor, Dorea, Blautia, and Subdoligranulum expressed spore proteins. Firmicutes (Faecalibacterium, Butyrivibrio, Megasphaera, Subdoligranulum, Oscillibacter, Anaerostipes, and Anaerotruncus) expressed enzymes required for butyrate production. Megamonas, Phascolarctobacterium, and Blautia (exceptions from the phylum Firmicutes) and all Bacteroidetes expressed enzymes for propionate production pathways. Representatives of Bacteroidetes also expressed xylose isomerase, enzymes required for polysaccharide degradation, and ExbBD, TonB, and outer membrane receptors likely to be involved in oligosaccharide transport. Based on our data, Anaerostipes, Anaerotruncus, and Subdoligranulum might be optimal probiotic strains, since these represent spore-forming butyrate producers. However, certain care should be taken during microbiota transplantation because the microbiota may behave differently in the intestinal tract of a recipient depending on how well the existing communities are established.
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38
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Choi KY, Lee TK, Sul WJ. Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1217-25. [PMID: 26323514 PMCID: PMC4554860 DOI: 10.5713/ajas.15.0026] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/23/2015] [Accepted: 03/31/2015] [Indexed: 02/01/2023]
Abstract
Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.
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Affiliation(s)
- Ki Young Choi
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
| | - Woo Jun Sul
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
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Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. Metaproteomic analysis using the Galaxy framework. Proteomics 2015; 15:3553-65. [DOI: 10.1002/pmic.201500074] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/25/2015] [Accepted: 06/04/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Pratik D. Jagtap
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Kevin Murray
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Joel Kooren
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Nelson L. Rhodus
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Joel Rudney
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Timothy J. Griffin
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
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40
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Arul AB, Byambadorj M, Han NY, Park JM, Lee H. Development of an Automated, High-throughput Sample Preparation Protocol for Proteomics Analysis. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Albert-Baskar Arul
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | | | - Na-Young Han
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | - Jong Moon Park
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | - Hookeun Lee
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy; Gachon University; Incheon 406-799 Republic of Korea
- Gachon Medical Research Institute; Gil Medical Center; Incheon 405-760 Republic of Korea
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Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S. Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics 2015; 15:3474-85. [PMID: 25677681 DOI: 10.1002/pmic.201400573] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/05/2015] [Indexed: 02/03/2023]
Abstract
To date, most metaproteomic studies of the gut microbiota employ stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how, and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged. Protein extracts were then processed by filter-aided sample preparation, single-run LC, and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the nonmicrobial components (host and food) when compared to not centrifuged. Nevertheless, dramatic differences in the relative abundance of several gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, some important microbial functional categories, including cell surface enzymes, membrane-associated proteins, extracellular proteins, and flagella, were significantly reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed. All MS data have been deposited in the ProteomeXchange with identifier PXD001573 (http://proteomecentral.proteomexchange.org/dataset/PXD001573).
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Affiliation(s)
| | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Tramariglio, Alghero, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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Mao L, Franke J. Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring. Proteomics 2014; 15:1142-51. [DOI: 10.1002/pmic.201400329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Lei Mao
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
| | - Jacqueline Franke
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
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Deusch S, Tilocca B, Camarinha-Silva A, Seifert J. News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals. Comput Struct Biotechnol J 2014; 13:55-63. [PMID: 26900430 PMCID: PMC4720016 DOI: 10.1016/j.csbj.2014.12.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 12/20/2022] Open
Abstract
Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about the investigated microbiota. In general, integration of the main Omics-technologies (genomics, transcriptomics, proteomics and metabolomics) in live science promises highly detailed information about the specific research object and helps to understand molecular changes in response to internal and external environmental factors. The microbial communities settled in the mammalian gastrointestinal tract are essential for the host metabolism and have a major impact on its physiology and health. The microbiotas of livestock like chicken, pig and ruminants are becoming a focus of interest for veterinaries, animal nutritionists and microbiologists. While pig is more often used as an animal model for human-related studies, the rumen microbiota harbors a diversity of enzymes converting complex carbohydrates into monomers which bears high potential for biotechnological applications. This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.
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Affiliation(s)
| | | | | | - Jana Seifert
- Corresponding author at: University of Hohenheim, Institute of Animal Nutrition, Emil-Wolff-Str. 10, 70599 Stuttgart, Germany.
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Tanca A, Palomba A, Pisanu S, Deligios M, Fraumene C, Manghina V, Pagnozzi D, Addis MF, Uzzau S. A straightforward and efficient analytical pipeline for metaproteome characterization. MICROBIOME 2014; 2:49. [PMID: 25516796 PMCID: PMC4266899 DOI: 10.1186/s40168-014-0049-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/11/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically enables the transition from assessing the genomic potential to actually measuring the functional expression of a microbiome. However, significant research efforts are still required to develop analysis pipelines optimized for metaproteome characterization. RESULTS This work presents an efficient analytical pipeline for shotgun metaproteomic analysis, combining bead-beating/freeze-thawing for protein extraction, filter-aided sample preparation for cleanup and digestion, and single-run liquid chromatography-tandem mass spectrometry for peptide separation and identification. The overall procedure is more time-effective and less labor-intensive when compared to state-of-the-art metaproteomic techniques. The pipeline was first evaluated using mock microbial mixtures containing different types of bacteria and yeasts, enabling the identification of up to over 15,000 non-redundant peptide sequences per run with a linear dynamic range from 10(4) to 10(8) colony-forming units. The pipeline was then applied to the mouse fecal metaproteome, leading to the overall identification of over 13,000 non-redundant microbial peptides with a false discovery rate of <1%, belonging to over 600 different microbial species and 250 functionally relevant protein families. An extensive mapping of the main microbial metabolic pathways actively functioning in the gut microbiome was also achieved. CONCLUSIONS The analytical pipeline presented here may be successfully used for the in-depth and time-effective characterization of complex microbial communities, such as the gut microbiome, and represents a useful tool for the microbiome research community.
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Affiliation(s)
- Alessandro Tanca
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Antonio Palomba
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Salvatore Pisanu
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Massimo Deligios
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Cristina Fraumene
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Valeria Manghina
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Daniela Pagnozzi
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Maria Filippa Addis
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Sergio Uzzau
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
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Yu Y, Suh MJ, Sikorski P, Kwon K, Nelson KE, Pieper R. Urine sample preparation in 96-well filter plates for quantitative clinical proteomics. Anal Chem 2014; 86:5470-7. [PMID: 24797144 PMCID: PMC4045327 DOI: 10.1021/ac5008317] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/05/2014] [Indexed: 01/03/2023]
Abstract
Urine is an important, noninvasively collected body fluid source for the diagnosis and prognosis of human diseases. Liquid chromatography mass spectrometry (LC-MS) based shotgun proteomics has evolved as a sensitive and informative technique to discover candidate disease biomarkers from urine specimens. Filter-aided sample preparation (FASP) generates peptide samples from protein mixtures of cell lysate or body fluid origin. Here, we describe a FASP method adapted to 96-well filter plates, named 96FASP. Soluble urine concentrates containing ~10 μg of total protein were processed by 96FASP and LC-MS resulting in 700-900 protein identifications at a 1% false discovery rate (FDR). The experimental repeatability, as assessed by label-free quantification and Pearson correlation analysis for shared proteins among replicates, was high (R ≥ 0.97). Application to urinary pellet lysates which is of particular interest in the context of urinary tract infection analysis was also demonstrated. On average, 1700 proteins (±398) were identified in five experiments. In a pilot study using 96FASP for analysis of eight soluble urine samples, we demonstrated that protein profiles of technical replicates invariably clustered; the protein profiles for distinct urine donors were very different from each other. Robust, highly parallel methods to generate peptide mixtures from urine and other body fluids are critical to increase cost-effectiveness in clinical proteomics projects. This 96FASP method has potential to become a gold standard for high-throughput quantitative clinical proteomics.
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Affiliation(s)
- Yanbao Yu
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Moo-Jin Suh
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Patricia Sikorski
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Keehwan Kwon
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Karen E. Nelson
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rembert Pieper
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
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