251
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Pandit RJ, Hinsu AT, Patel NV, Koringa PG, Jakhesara SJ, Thakkar JR, Shah TM, Limon G, Psifidi A, Guitian J, Hume DA, Tomley FM, Rank DN, Raman M, Tirumurugaan KG, Blake DP, Joshi CG. Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing. MICROBIOME 2018; 6:115. [PMID: 29935540 PMCID: PMC6015460 DOI: 10.1186/s40168-018-0501-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/13/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. METHODS Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing. RESULTS Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations. CONCLUSION Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota.
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Affiliation(s)
- Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Ankit T Hinsu
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Namrata V Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Georgina Limon
- Department of Pathology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Androniki Psifidi
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
- Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Javier Guitian
- Department of Pathology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - David A Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Fiona M Tomley
- Department of Pathology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Dharamshibhai N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - M Raman
- Department of Veterinary Parasitology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600007, India
| | - K G Tirumurugaan
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600051, India
| | - Damer P Blake
- Department of Pathology and Population Sciences, Royal Veterinary College, North Mymms, Hertfordshire, UK.
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
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252
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Regulation of CD4 +CD8 -CD25 + and CD4 +CD8 +CD25 + T cells by gut microbiota in chicken. Sci Rep 2018; 8:8627. [PMID: 29872084 PMCID: PMC5988814 DOI: 10.1038/s41598-018-26763-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/18/2018] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota in chicken has long been studied, mostly from the perspective of growth performance. However, there are some immunological studies regarding gut homeostasis in chicken. Although CD4+CD25+ T cells are reported to act as regulatory T cells (Tregs) in chicken, there have been no studies showing the relationship between gut microbiota and Tregs. Therefore, we established a model for 'antibiotics (ABX)-treated chickens' through administration of an antibiotic cocktail consisting of ampicillin, gentamycin, neomycin, metronidazole, and vancomycin in water for 7 days. CD4+CD8-CD25+ and CD4+CD8+CD25+ T cells in cecal tonsils were significantly decreased in this model. Gram-positive bacteria, especially Clostridia, was responsible for the changes in CD4+CD8-CD25+ or CD4+CD8+CD25+ T cells in cecal tonsils. Feeding ABX-treated chickens with acetate recovered CD4+CD8-CD25+ and CD4+CD8+CD25+ T cells in cecal tonsils. GPR43, a receptor for acetate, was highly expressed in CD4+CD8-CD25+ T cells. In conclusion, our study demonstrated that the gut microbiota can regulate the population of CD4+CD8-CD25+ and CD4+CD8+CD25+ T cells, and that acetate is responsible for the induction of CD4+CD8-CD25+ T cells in cecal tonsils via GPR43.
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253
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Yausheva Е, Miroshnikov S, Sizova Е. Intestinal microbiome of broiler chickens after use of nanoparticles and metal salts. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:18109-18120. [PMID: 29691748 DOI: 10.1007/s11356-018-1991-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
The research included the study of influence of ultrafine particle preparations (nanoparticles of copper, zinc, iron, CuZn alloy) and metal salts (iron pyrophosphate, copper asparginate, zinc asparginate) on the composition of cecal microbiota of broiler chickens. Before adding the studied nanoparticles and metal salts to the diet, cecal microbiota of broiler chickens was represented by 76% Firmicutes taxon and 16% Bacteroidetes. Numerous among them were the bacteria of the taxa Anaerotruncus spp., Lactobacillus spp., Blautia spp., Alistipes spp., and Bacteroides spp.; they constituted 18, 17, 11, and 6%, respectively. A peculiarity of action of the most analyzed metals in nanoform and in the form of salts was a decrease in the number of phylum Firmicutes bacteria and an increase in the number of microorganisms of the phylum Bacteroidetes. The number of bacteria belonging to the families Ruminococcaceae (III, IV, V, VII, and VIII groups), Bacteroidaceae (in all experimental groups), and Lachnospiraceae (I, IV, V, and VII groups) was registered within the taxa of Firmicutes and Bacteroidetes. At the same time, in some experimental groups, the number of bacteria of the family Lachnospiraceae (II, III, and VIII) decreased in the intestine. The data obtained can be used to assess the possibility of using metal nanoparticles in the poultry diet, as a micronutrient preparation, to correct dysbiosis and to improve the utilization of fodder energy.
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Affiliation(s)
- Еlena Yausheva
- State Educational Institution All-Russian Research Institute of Beef Cattle Breeding, 29, 9-Yanvarya Street, Orenburg, Russia, 460000
| | - Sergey Miroshnikov
- State Educational Institution All-Russian Research Institute of Beef Cattle Breeding, 29, 9-Yanvarya Street, Orenburg, Russia, 460000
| | - Еlena Sizova
- State Educational Institution All-Russian Research Institute of Beef Cattle Breeding, 29, 9-Yanvarya Street, Orenburg, Russia, 460000.
- Orenburg State University, Pobedy pr. 13, Orenburg, Russia, 460018.
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254
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A Consistent and Predictable Commercial Broiler Chicken Bacterial Microbiota in Antibiotic-Free Production Displays Strong Correlations with Performance. Appl Environ Microbiol 2018; 84:AEM.00362-18. [PMID: 29625981 DOI: 10.1128/aem.00362-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/02/2018] [Indexed: 11/20/2022] Open
Abstract
Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and Lactobacillus was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production.IMPORTANCE Multidrug-resistant bacterial pathogens are perhaps the greatest medical challenge we will face in the 21st century and beyond. Antibiotics are necessary in animal production to treat disease. As such, animal production is a contributor to the problem of antibiotic resistance. Efforts are underway to reduce antibiotic use in animal production. However, we are also challenged to feed the world's increasing population, and sustainable meat production is paramount to providing a safe and quality protein source for human consumption. In the absence of antibiotics, alternative approaches are needed to maintain health and prevent disease, and probiotics have great promise as one such approach. This work paves the way for the development of alternative approaches to raising poultry by increasing our understandings of what defines the poultry microbiome and of how it can potentially be modulated to improve animal health and performance.
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255
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Bortoluzzi C, Pedroso AA, Mallo JJ, Puyalto M, Kim WK, Applegate TJ. Sodium butyrate improved performance while modulating the cecal microbiota and regulating the expression of intestinal immune-related genes of broiler chickens. Poult Sci 2018; 96:3981-3993. [PMID: 29050425 DOI: 10.3382/ps/pex218] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
This study evaluated the effect of sodium butyrate (SB) on performance, expression of immune-related genes in the cecal tonsils, and cecal microbiota of broiler chickens when dietary energy and amino acids concentrations were reduced. Day-old male Ross 708 broiler chicks were fed dietary treatments in a 3 × 2 factorial design (8 pens per treatment) with 3 dietary formulations (control diet; reduction of 2.3% of amino acids and 60 kcal/kg; and reduction of 4.6% of amino acids and 120 kcal/kg) with or without the inclusion of 0.1% of SB. Feed intake (FI), body weight gain (BW gain), and feed conversion ratio (FCR) were recorded until 28 d of age. From 14 to 28 d, there was an interaction of nutrient density by SB (P = 0.003) wherein BW gain of birds fed SB was impaired less by the energy/amino acids reduction than unsupplemented birds. A similar result was obtained from 1 to 28 d (P = 0.004). No interaction (P < 0.05) between nutrient density by SB was observed for FCR. Nutritional density of the diets and SB modified the structure, composition, and predicted function of the cecal microbiota. The nutritionally reduced diet altered the imputed function performed by the microbiota and the SB supplementation reduced these variations, keeping the microbial function similar to that observed in chickens fed a control diet. The frequency of bacterial species presenting the butyryl-CoA: acetate CoA-transferase gene increased in the microbiota of chickens fed a nutritionally reduced diet without SB supplementation, and was not changed by nutrient density of the diet when supplemented with SB (interaction; P = 0.01). SB modulated the expression of immune related genes in the cecal tonsils; wherein SB upregulated the expression of A20 in broilers fed control diets (P < 0.05) and increased IL-6 expression (P < 0.05). These results show that SB had positive effects on the productive performance of broilers fed nutritionally reduced diets, partially by modulating the cecal microbiota and exerting immune-modulatory effects.
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Affiliation(s)
- C Bortoluzzi
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907.,Department of Poultry Science, University of Georgia, Athens, GA, 30602
| | | | | | | | - W K Kim
- Department of Poultry Science, University of Georgia, Athens, GA, 30602
| | - T J Applegate
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907.,Department of Poultry Science, University of Georgia, Athens, GA, 30602
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256
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D'Andreano S, Sànchez Bonastre A, Francino O, Cuscó Martí A, Lecchi C, Grilli G, Giovanardi D, Ceciliani F. Gastrointestinal microbial population of turkey (Meleagris gallopavo) affected by hemorrhagic enteritis virus. Poult Sci 2018; 96:3550-3558. [PMID: 28938792 DOI: 10.3382/ps/pex139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/09/2017] [Indexed: 12/27/2022] Open
Abstract
Hemorrhagic enteritis (HE) is an acute viral disease that affects avian species, particularly turkeys, compromising their commercial production and having a negative effect on animal welfare. Turkey adenovirus 3 (TAdV-3), is the main causal agent of the disease. In this study, we considered 3 groups of turkeys to achieve 2 purposes: 1) A preliminary investigation on the microbiota content in the 4 parts of healthy turkey's intestine (group A), namely duodenum, jejunum, ileum, and ceca was done; 2) an investigation on the relationship between natural infections with TAdV-3 and the intestinal microbiota in the jejunum, where HE mostly develops, comparing group A with animals with molecular positivity for the virus and with clinical signs of HE (group B) and animals with molecular positivity for the virus but without clinical signs (group C). Massive sequencing of the hypervariable V1-V2 regions of 16S rRNA gene and QIIME 1.9.1 software analysis was performed, and operation taxonomic units (OTUs) were classified into 4 abundant phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The microbial population of small intestine was distributed almost homogeneously in the healthy turkeys, and Firmicutes was the prevalent phylum (79.85% in duodenum, 89.57% in jejunum and 99.28% in ileum). As compared with small intestine, ceca microbial community was much more heterogeneous: Firmicutes (48.03%), Bacteroidetes (33.60%) and Proteobacteria (12.32%). In the natural infections of HEV, the main bacterial families were Bacteroidaceae (Bacteroidetes) and Peptostreptococcaceae (Firmicutes), uniquely detected in group B and C. Also Clostridiaceae (Firmicutes) was detected, uniquely in group B.
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Affiliation(s)
- Sara D'Andreano
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, 08193 Bellaterra, Spain.,Molecular Genetics Veterinary Service, Veterinary School, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Armand Sànchez Bonastre
- Molecular Genetics Veterinary Service, Veterinary School, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service, Veterinary School, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Cuscó Martí
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, 08193 Bellaterra, Spain.,Molecular Genetics Veterinary Service, Veterinary School, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cristina Lecchi
- Department of Veterinary Science, Università di Milano, Via Celoria 10, 20133 Milano
| | - Guido Grilli
- Department of Veterinary Science, Università di Milano, Via Celoria 10, 20133 Milano
| | - Davide Giovanardi
- Laboratorio Tre Valli, Viale A.Veronesi 5, 37132 San Michele Extra, Verona, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Science, Università di Milano, Via Celoria 10, 20133 Milano
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257
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Olsen R, Kudirkiene E, Thøfner I, Pors S, Karlskov-Mortensen P, Li L, Papasolomontos S, Angastiniotou C, Christensen J. Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load. Poult Sci 2018; 96:3901-3911. [PMID: 29050418 DOI: 10.3382/ps/pex182] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/13/2017] [Indexed: 11/20/2022] Open
Abstract
Disinfection of hatching eggs is essential to ensure high quality production of broilers. Different protocols are followed in different hatcheries; however, only limited scientific evidence on how the disinfection procedures impact the microbiome is available. The aim of the present study was to characterize the microbiome and aerobic bacterial load of hatching eggs before disinfection and during the subsequent disinfection steps. The study included a group of visibly clean and a group of visibly dirty eggs. For dirty eggs, an initial wash in chlorine was performed, hereafter all eggs were submitted to two times fumigation and finally spray disinfection. The eggshell microbiome was characterized by sequencing of the total amount of 16S rRNA extracted from each sample, consisting of shell surface swabs of five eggs from the same group. In addition, the number of colony forming units (cfu) under aerobic conditions was established for each disinfection step. The disinfection procedure reduced the bacterial load from more than 104 cfu (initially visibly clean eggs) and 105 cfu (initially visibly dirty eggs) to less than 10 cfu per sample after disinfection for both groups of eggs. The microbiome of both initially visibly clean and initially visibly dirty eggs had the highest abundances of the phyla Firmicutes, Proteobacteria and Bacteroidetes. Within the phyla Firmicutes the relative abundances of Clostridiales decreased while Lactobacillus increased from before to after final disinfection. In conclusion, the investigated disinfection procedure is effective in reducing the bacterial load, and by adding a chlorine wash for initially visibly dirty eggs, the microbiome of initially visibly clean and initially visibly dirty eggs had a highly similar microflora after the final disinfection step.
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Affiliation(s)
- R Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - E Kudirkiene
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - I Thøfner
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - S Pors
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - P Karlskov-Mortensen
- Department of Veterinary Clinical and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - L Li
- College of Light Industry and Food Sciences, South China University of Technology, China
| | | | | | - J Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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258
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Qin C, Gong L, Zhang X, Wang Y, Wang Y, Wang B, Li Y, Li W. Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broilers. ACTA ACUST UNITED AC 2018; 4:358-366. [PMID: 30564755 PMCID: PMC6284224 DOI: 10.1016/j.aninu.2018.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 01/06/2023]
Abstract
The gut microbiota plays important roles in animal overall health and productiveness. Balancing host gut microbiota by probiotics has been documented. Our previous study showed that Saccharomyces boulardii (Sb) and Bacillus subtilis B10 (Bs) significantly improve growth performance and modulate the intestinal histomorphology in broilers. To increase the knowledge regarding Sb and Bs, this study investigated the effects of these 2 probiotic strains on the gut microbiota in broilers. Three hundred 1-day-old Sanhuang broilers (Chinese cross breed) were randomly divided into 3 groups, each group with 5 replications (n = 20). The control group (CK) was fed a basal diet containing an antibiotic (virginiamycin, 20 mg/kg) and the other 2 groups received Sb and Bs (1 × 108 cfu/kg of feed) in addition to the basal diet. After 72 d of treatment, pyrosequencing revealed that the bacterial communities varied along the section of intestinal tract in the control and Bs groups, but not in the Sb group. No difference in microbial diversity was observed among 3 groups. The major phyla observed along the GI tract of broilers (particularly in the duodenum and cecum) were Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia, which were considered potentially growth performance-related. Bacteroidetes, Proteobacteria, and Verrucomicrobia were observed at a much higher abundance in the jejunums and ileums of the Sb group (P < 0.05). In addition, the jejunal microbial communities formed 3 different clusters at either the genus level or the category of metabolism among the groups, based on the principal component analyses. These data indicated that Sb and Bs can modulate the microbial ecosystem, and subsequently enhance the health status of broilers.
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Affiliation(s)
- Chubin Qin
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Li Gong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou 310012, China
| | - Yuanyuan Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yibin Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Baikui Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yali Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Weifen Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Science, Zhejiang University, Hangzhou 310058, China
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259
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A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0396-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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260
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Tannins and Bacitracin Differentially Modulate Gut Microbiota of Broiler Chickens. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1879168. [PMID: 29682522 PMCID: PMC5841071 DOI: 10.1155/2018/1879168] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/07/2017] [Accepted: 12/25/2017] [Indexed: 01/28/2023]
Abstract
Antibiotic growth promoters have been used for decades in poultry farming as a tool to maintain bird health and improve growth performance. Global concern about the recurrent emergence and spreading of antimicrobial resistance is challenging the livestock producers to search for alternatives to feed added antibiotics. The use of phytogenic compounds appears as a feasible option due to their ability to emulate the bioactive properties of antibiotics. However, detailed description about the effects of in-feed antibiotics and alternative natural products on chicken intestinal microbiota is lacking. High-throughput sequencing of 16S rRNA gene was used to study composition of cecal microbiota in broiler chickens supplemented with either bacitracin or a blend of chestnut and quebracho tannins over a 30-day grow-out period. Both tannins and bacitracin had a significant impact on diversity of cecal microbiota. Bacitracin consistently decreased Bifidobacterium while other bacterial groups were affected only at certain times. Tannins-fed chickens showed a drastic decrease in genus Bacteroides while certain members of order Clostridiales mainly belonging to the families Ruminococcaceae and Lachnospiraceae were increased. Different members of these groups have been associated with an improvement of intestinal health and feed efficiency in poultry, suggesting that these bacteria could be associated with productive performance of birds.
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261
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Banerjee S, Sar A, Misra A, Pal S, Chakraborty A, Dam B. Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Microbiology (Reading) 2018; 164:142-153. [PMID: 29393019 DOI: 10.1099/mic.0.000597] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sohini Banerjee
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
- Department of Environmental Studies, Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Arijit Misra
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Arindom Chakraborty
- Department of Statistics, Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
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262
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Lee KC, Kil DY, Sul WJ. Cecal microbiome divergence of broiler chickens by sex and body weight. J Microbiol 2017; 55:939-945. [DOI: 10.1007/s12275-017-7202-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/10/2017] [Accepted: 10/26/2017] [Indexed: 02/06/2023]
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263
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Antonissen G, Eeckhaut V, Van Driessche K, Onrust L, Haesebrouck F, Ducatelle R, Moore RJ, Van Immerseel F. Microbial shifts associated with necrotic enteritis. Avian Pathol 2017; 45:308-12. [PMID: 26950294 DOI: 10.1080/03079457.2016.1152625] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An outbreak of necrotic enteritis (NE) is a complex process requiring one or a number of predisposing factors rather than just the presence of pathogenic Clostridium perfringens. Examples are dietary influences, such as high levels of non-starch polysaccharides and fishmeal, and factors that evoke epithelial cell damage, such as Fusarium mycotoxins in feed and Eimeria infections. Recent studies have shown that different predisposing factors induce similar shifts in the intestinal microbiota composition. Butyrate-producing-strains of the Ruminococcaceae family are decreased in abundance by both fishmeal and Eimeria. Similarly, a decreased abundance of butyrate-producing-strains belonging to the Lachnospiraceae family has been induced by fishmeal. Also shifts are observed in the lactic acid-producing bacteria, such as decreased abundance of Lactobacillus johnsonii or Weissella confusa, when broilers were fed a fishmeal-based diet or a Fusarium mycotoxin contaminated diet. Finally, the abundance of Candidatus Savagella was decreased in broilers following Eimeria challenge or feeding a fumonisins contaminated diet. The nature of the microbiota shifts indicate that immune modulatory actions of the intestinal microbiota may play a critical role in the effect on the necrosis inducing activity of C. perfringens. Indeed, colonization with butyrate-producing bacteria plays a key role in counteracting inflammation in the gut and preserving intestinal integrity, while Candidatus Savagella is involved in stimulating Th17 and immunoglobulin A responses. Lactic acid bacteria stimulate colonization of lactate-utilizing and butyrate-producing Lachnospiraceae. Future research needs to clarify the role of the microbiota changes in the pathogenesis of NE.
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Affiliation(s)
- Gunther Antonissen
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium.,b Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Venessa Eeckhaut
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Karolien Van Driessche
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Lonneke Onrust
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Freddy Haesebrouck
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Richard Ducatelle
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
| | - Robert J Moore
- c School of Applied Sciences and Health Innovations Research Institute , RMIT University , Bundoora , Australia
| | - Filip Van Immerseel
- a Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine , Ghent University , Merelbeke , Belgium
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264
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Celi P, Cowieson A, Fru-Nji F, Steinert R, Kluenter AM, Verlhac V. Gastrointestinal functionality in animal nutrition and health: New opportunities for sustainable animal production. Anim Feed Sci Technol 2017. [DOI: 10.1016/j.anifeedsci.2017.09.012] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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265
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Macdonald SE, Nolan MJ, Harman K, Boulton K, Hume DA, Tomley FM, Stabler RA, Blake DP. Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology. PLoS One 2017; 12:e0184890. [PMID: 28934262 PMCID: PMC5608234 DOI: 10.1371/journal.pone.0184890] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
Eimeria species cause the intestinal disease coccidiosis, most notably in poultry. While the direct impact of coccidiosis on animal health and welfare is clear, its influence on the enteric microbiota and by-stander effects on chicken health and production remains largely unknown, with the possible exception of Clostridium perfringens (necrotic enteritis). This study evaluated the composition and structure of the caecal microbiome in the presence or absence of a defined Eimeria tenella challenge infection in Cobb500 broiler chickens using 16S rRNA amplicon sequencing. The severity of clinical coccidiosis in individual chickens was quantified by caecal lesion scoring and microbial changes associated with different lesion scores identified. Following E. tenella infection the diversity of taxa within the caecal microbiome remained largely stable. However, infection induced significant changes in the abundance of some microbial taxa. The greatest changes were detected in birds displaying severe caecal pathology; taxa belonging to the order Enterobacteriaceae were increased, while taxa from Bacillales and Lactobacillales were decreased with the changes correlated with lesion severity. Significantly different profiles were also detected in infected birds which remained asymptomatic (lesion score 0), with taxa belonging to the genera Bacteroides decreased and Lactobacillus increased. Many differential taxa from the order Clostridiales were identified, with some increasing and others decreasing in abundance in Eimeria-infected animals. The results support the view that caecal microbiome dysbiosis associated with Eimeria infection contributes to disease pathology, and could be a target for intervention to mitigate the impact of coccidiosis on poultry productivity and welfare. This work highlights that E. tenella infection has a significant impact on the abundance of some caecal bacteria with notable differences detected between lesion score categories emphasising the importance of accounting for differences in caecal lesions when investigating the relationship between E. tenella and the poultry intestinal microbiome.
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Affiliation(s)
- Sarah E. Macdonald
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
- * E-mail: (SEM); (DPB)
| | - Matthew J. Nolan
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Kimberley Harman
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Kay Boulton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - David A. Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Fiona M. Tomley
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Richard A. Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Damer P. Blake
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
- * E-mail: (SEM); (DPB)
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266
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García-Aljaro C, Ballesté E, Muniesa M, Jofre J. Determination of crAssphage in water samples and applicability for tracking human faecal pollution. Microb Biotechnol 2017; 10:1775-1780. [PMID: 28925595 PMCID: PMC5658656 DOI: 10.1111/1751-7915.12841] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/15/2022] Open
Abstract
In recent decades, considerable effort has been devoted to finding microbial source-tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage-derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 106 GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction. In wastewaters containing animal faecal remains, 39% of the samples were negative for the presence of the crAssphage sequence, while those showing positive results (41% of the samples) were at least 1 log10 unit lower than the samples of human origin. Noteworthy, the log10 values of the ratio (R) crAssphage (GC/ml)/Escherichia coli (CFU/ml) varied significantly depending on the human or animal origin (R > 1.5 for human samples and R < -1.5 for animal wastewater samples. This study opens the way for further research to explore if different specific animal variants of crAssphage exist and whether other zones of the crAssphage genome are better suited to source discrimination.
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Affiliation(s)
- Cristina García-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Elisenda Ballesté
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
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267
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Reed S, Neuman H, Glahn RP, Koren O, Tako E. Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet. PLoS One 2017; 12:e0182431. [PMID: 28796793 PMCID: PMC5552115 DOI: 10.1371/journal.pone.0182431] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/18/2017] [Indexed: 12/20/2022] Open
Abstract
Biofortification is a plant breeding method that introduces increased concentrations of minerals in staple food crops (e.g., legumes, cereal grains), and has shown success in alleviating insufficient Fe intake in various human populations. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification have not yet been reported, although the consumption of Fe biofortified staple food crops has increased significantly over time. Hence, in this study, we performed a 6-week feeding trial in Gallus gallus (n = 14), aimed to investigate the alterations in the gut microbiome following administration of an Fe biofortified bean-based diet (biofortified, BFe) versus a bean based diet with poorly-bioavailable Fe (standard, SFe). Cream seeded carioca bean based diets were designed in an identical fashion to those used in a recent human clinical trial of Fe biofortified beans in Rwanda. We hypothesized that the different dietary Fe contents in the beans based diets will alter the composition and function of the intestinal microbiome. The primary outcomes were changes in the gut microbiome composition and function analyzed by 16S rRNA gene sequencing. We observed no significant changes in phylogenetic diversity between groups. There were significant differences in the composition of the microbiota between groups, with the BFe group harboring fewer taxa participating in bacterial Fe uptake, increased abundance of bacteria involved in phenolic catabolism, and increased abundance of beneficial butyrate-producing bacteria. Additionally, depletion of key bacterial pathways responsible for bacterial viability and Fe uptake suggest that improvements in Fe bioavailability, in addition to increases in Fe-polyphenol and Fe-phytate complexes due to biofortification, led to decreased concentrations of cecal Fe available for bacterial utilization. Our findings demonstrate that Fe biofortification may improve Fe status without negatively altering the structure and function of the gut microbiota, as is observed with other nutritional methods of Fe supplementation. These results may be used to further improve the efficacy and safety of future biofortification efforts in eradicating global Fe deficiency.
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Affiliation(s)
- Spenser Reed
- USDA-ARS Robert W. Holley Center for Agriculture & Health, Cornell University, Ithaca, NY, United States of America
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States of America
| | - Hadar Neuman
- Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Raymond P. Glahn
- USDA-ARS Robert W. Holley Center for Agriculture & Health, Cornell University, Ithaca, NY, United States of America
| | - Omry Koren
- Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Elad Tako
- USDA-ARS Robert W. Holley Center for Agriculture & Health, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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268
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Disruption in the cecal microbiota of chickens challenged with Clostridium perfringens and other factors was alleviated by Bacillus licheniformis supplementation. PLoS One 2017; 12:e0182426. [PMID: 28771569 PMCID: PMC5542615 DOI: 10.1371/journal.pone.0182426] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 07/18/2017] [Indexed: 02/02/2023] Open
Abstract
Clostridium perfringens can induce necrotic enteritis of chickens, which causes large economic losses every year. Bacillus licheniformis, a probiotic, can inhibit the growth of pathogenic bacteria such as Clostridium perfringens, thereby improving the health status of chickens. However, from a microbial ecology perspective, the mechanisms by which alterations to the gut microbiota improve health remain unknown. In this study, we used Illumina MiSeq sequencing to investigate the cecal microbiota of a negative control group (NC), a C. perfringens and Eimeria challenge group with fishmeal supplementation (PC), a group supplemented with fishmeal and infected with coccidia (FC), and group PC with B. licheniformis supplementation (BL). We found that the health status of C. perfringens-challenged chickens was compromised, and that B. licheniformis improved the growth of the chickens challenged with pathogens. Microbial diversity analysis and taxonomic profiling of groups NC, PC, and FC revealed a disturbed cecal microflora of the birds with C. perfringens. We also characterized the microbiota of the chickens in the BL group using several methods. Principal coordinate analysis demonstrated that, compared with group PC, the bacterial community structure of group BL was more similar to that of group NC. Linear discriminant analysis with effect size revealed less differentially represented bacterial taxa between groups BL and NC than between groups PC and NC. In addition, groups BL and NC appeared to have similar overrepresented microbial taxa (such as Bacteroides, Helicobacter, Megamonas, and Akkermansia) compared with group PC. Finally, a phylogenetic investigation of communities by reconstruction of unobserved states analysis indicated that large differences existed between group PC and groups NC and BL. In conclusion, pre-treatment with B. licheniformis reduced the disturbance of the cecal microbiome induced by challenge with C. perfringens and other factors in broiler chickens.
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269
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Brown CM, Staley C, Wang P, Dalzell B, Chun CL, Sadowsky MJ. A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8263-8271. [PMID: 28640599 DOI: 10.1021/acs.est.7b01353] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Current microbial source-tracking (MST) methods, employed to determine sources of fecal contamination in waterways, use molecular markers targeting host-associated bacteria in animal or human feces. However, there is a lack of knowledge about fecal microbiome composition in several animals and imperfect marker specificity and sensitivity. To overcome these issues, a community-based MST method has been developed. Here, we describe a study done in the Lake Superior-Saint Louis River estuary using SourceTracker, a program that calculates the source contribution to an environment. High-throughput DNA sequencing of microbiota from a diverse collection of fecal samples obtained from 11 types of animals (wild, agricultural, and domesticated) and treated effluent (n = 233) was used to generate a fecal library to perform community-based MST. Analysis of 319 fecal and environmental samples revealed that the community compositions in water and fecal samples were significantly different, allowing for the determination of the presence of fecal inputs and identification of specific sources. SourceTracker results indicated that fecal bacterial inputs into the Lake Superior estuary were primarily attributed to wastewater effluent and, to a lesser extent, geese and gull wastes. These results suggest that a community-based MST method may be another useful tool for determining sources of aquatic fecal bacteria.
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Affiliation(s)
- Clairessa M Brown
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
| | - Christopher Staley
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
| | - Ping Wang
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
| | - Brent Dalzell
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
| | - Chan Lan Chun
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
| | - Michael J Sadowsky
- BioTechnology Institute and ‡Department of Soil, Water, and Climate, University of Minnesota , Saint Paul, Minnesota 55455, United States
- Natural Resources Research Institute and ∥Department of Civil Engineering, University of Minnesota Duluth , Duluth, Minnesota 55812, United States
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270
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Kobierecka PA, Wyszyńska AK, Aleksandrzak-Piekarczyk T, Kuczkowski M, Tuzimek A, Piotrowska W, Górecki A, Adamska I, Wieliczko A, Bardowski J, Jagusztyn-Krynicka EK. In vitro characteristics of Lactobacillus spp. strains isolated from the chicken digestive tract and their role in the inhibition of Campylobacter colonization. Microbiologyopen 2017; 6. [PMID: 28736979 PMCID: PMC5635155 DOI: 10.1002/mbo3.512] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 02/07/2023] Open
Abstract
Campylobacter jejuni/coli infections are the leading cause of bacterial diarrheal illnesses in humans. Many epidemiological studies indicate that improperly prepared meat from chickens that carry a high load of Campylobacter in their intestinal tracts is the key source of human infections. LAB, mainly members of the Lactococcus and Lactobacillus genera, increasingly have been tested as vehicles for the delivery of heterologous bacterial or viral antigens to animal mucosal immune systems. Thus, the objective of this study was to isolate, identify, and characterize Lactobacillus spp. strains isolated from chickens bred in Poland. Their ability to decrease the level of bird gut colonization by C. jejuni strain was also analyzed. First, the influence of the different chicken rearing systems was evaluated, especially the effect of diets on the Lactobacillus species that colonize the gut of chickens. Next, selected strains were analyzed in terms of their anti‐Campylobacter activity in vitro; potential probiotic traits such as adhesion properties, bile and low pH tolerance; and their ability to grow on a defined carbon source. Given that improperly prepared chicken meat is the main source of human infection by Campylobacter, the selected strains were also assessed for their ability to inhibit Campylobacter colonization in the bird's intestine. These experiments revealed enormous physiological diversity among the Lactobacillus genus strains. Altogether, our results showed that L. plantarum strains isolated from the digestive tracts of chickens bred in Poland displayed some probiotic attributes in vitro and were able to decrease the level of bird gut colonization by C. jejuni strain. This suggests that they can be employed as vectors to deliver Campylobacter immunodominant proteins to the bird's immune system to strengthen the efficacy of in ovo vaccination.
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Affiliation(s)
- Patrycja A Kobierecka
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Agnieszka K Wyszyńska
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | | | - Maciej Kuczkowski
- Faculty of Veterinary Medicine, Department of Epizootiology and the Clinic of Birds and Exotic Animals, University of Environmental and Life Sciences, Wrocław, Poland
| | - Anna Tuzimek
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Wioletta Piotrowska
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Adrian Górecki
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Iwona Adamska
- Faculty of Biology, Department of Animal Physiology, Institute of Zoology, University of Warsaw, Warsaw, Poland
| | - Alina Wieliczko
- Faculty of Veterinary Medicine, Department of Epizootiology and the Clinic of Birds and Exotic Animals, University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Bardowski
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Elżbieta K Jagusztyn-Krynicka
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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271
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Mink (Mustela vison) Gut Microbial Communities from Northeast China and Its Internal Relationship with Gender and Food Additives. Curr Microbiol 2017; 74:1169-1177. [DOI: 10.1007/s00284-017-1301-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/05/2017] [Indexed: 01/26/2023]
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272
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Pechar R, Killer J, Švejstil R, Salmonová H, Geigerová M, Bunešová V, Rada V, Benada O. Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica). Int J Syst Evol Microbiol 2017; 67:2403-2411. [DOI: 10.1099/ijsem.0.001972] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Bunešová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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273
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Park S, Roto S, Pavlidis H, McIntyre D, Striplin K, Brammer L, Ricke S. Effects of feeding Original XPC™ to broilers with a live coccidiosis vaccine under industrial conditions: Part 2. Cecal microbiota analysis. Poult Sci 2017; 96:2400-2411. [DOI: 10.3382/ps/pex014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/04/2017] [Indexed: 12/17/2022] Open
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274
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Wilkinson TJ, Cowan AA, Vallin HE, Onime LA, Oyama LB, Cameron SJ, Gonot C, Moorby JM, Waddams K, Theobald VJ, Leemans D, Bowra S, Nixey C, Huws SA. Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys. Front Microbiol 2017; 8:1089. [PMID: 28690591 PMCID: PMC5479886 DOI: 10.3389/fmicb.2017.01089] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/30/2017] [Indexed: 12/11/2022] Open
Abstract
The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.
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Affiliation(s)
- Toby J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - A A Cowan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - H E Vallin
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - L A Onime
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Linda B Oyama
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - S J Cameron
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom.,Department of Surgery and Cancer, Faculty of Medicine, Imperial College LondonLondon, United Kingdom
| | - Charlotte Gonot
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - J M Moorby
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - K Waddams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - V J Theobald
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - D Leemans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - S Bowra
- Phytatec (UK) Ltd.-Plas GogerddanAberystwyth, United Kingdom
| | - C Nixey
- British Poultry CouncilLondon, United Kingdom
| | - Sharon A Huws
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
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275
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Park SH, Kim SA, Lee SI, Rubinelli PM, Roto SM, Pavlidis HO, McIntyre DR, Ricke SC. Original XPC TM Effect on Salmonella Typhimurium and Cecal Microbiota from Three Different Ages of Broiler Chickens When Incubated in an Anaerobic In Vitro Culture System. Front Microbiol 2017; 8:1070. [PMID: 28659891 PMCID: PMC5468444 DOI: 10.3389/fmicb.2017.01070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/29/2017] [Indexed: 01/29/2023] Open
Abstract
Feed supplements are utilized in the poultry industry as a means for improving growth performance and reducing pathogens. The aim of the present study was to evaluate the effects of Diamond V Original XPCTM (XPC, a fermented product generated from yeast cultures) on Salmonella Typhimurium ST 97 along with its potential for modulation of the cecal microbiota by using an anaerobic in vitro mixed culture assay. Cecal slurries obtained from three broiler chickens at each of three sampling ages (14, 28, and 42 days) were generated and exposed to a 24 h pre-incubation period with the various treatments: XPC (1% XPC, ceca, and feeds), CO (ceca only), and NC (negative control) group consisting of ceca and feeds. The XPC, CO, and NC were each challenged with S. Typhimurium and subsequently plated on selective media at 0, 24, and 48 h. Plating results indicated that the XPC treatment significantly reduced the survival of S. Typhimurium at the 24 h plating time point for both the 28 and 42 days bird sampling ages, while S. Typhimurium reduction in the NC appeared to eventually reach the same population survival level at the 48 h plating time point. For microbiome analysis, Trial 1 revealed that XPC, CO, and NC groups exhibited a similar pattern of taxa summary. However, more Bacteroidetes were observed in the CO group at 24 and 48 h. There were no significant differences (P > 0.05) in alpha diversity among samples based on day, hour and treatment. For beta diversity analysis, a pattern shift was observed when samples clustered according to sampling hour. In Trial 2, both XPC and NC groups exhibited the highest Firmicutes level at 0 h but the Bacteroidetes group became dominant at 6 h. Complexity of alpha diversity was increased in the initial contents from older birds and became less complex after 6 h of incubation. Beta diversity analysis was clustered as a function of treatment NC and XPC groups and by individual hours including 6, 12, 24, and 48 h. Overall, addition of XPC influenced microbiome diversity in a similar fashion to the profile of the NC group.
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Affiliation(s)
- Si Hong Park
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
| | - Sun Ae Kim
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
| | - Sang In Lee
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
| | - Peter M. Rubinelli
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
| | - Stephanie M. Roto
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
| | | | | | - Steven C. Ricke
- Center for Food Safety and Department of Food Science, University of Arkansas, FayettevilleAR, United States
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276
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Zhou Z, Nie K, Huang Q, Li K, Sun Y, Zhou R, Wang Z, Hu S. Changes of cecal microflora in chickens following Eimeria tenella challenge and regulating effect of coated sodium butyrate. Exp Parasitol 2017; 177:73-81. [PMID: 28455119 DOI: 10.1016/j.exppara.2017.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 04/10/2017] [Accepted: 04/23/2017] [Indexed: 12/18/2022]
Abstract
Eimeria tenella, one of the most important parasitic protozoa in the genus Eimeria, is responsible for chicken caecal coccidiosis resulting in huge economic losses to poultry industry. The present study investigated the changes in caecal microflora of E. tenella-infected chickens and the regulating effect of coated sodium butyrate, a potential alternative to antibiotics. Using high-throughput sequencing of 16S rRNA V3-V4 region of bacteria we found significant changes in caecal microflora of E. tenella-infected chickens indicated by an increase of Firmicutes (mainly Ruminococcaceae, Lachnospiraceae and vadin BB60) and Proteobacteria (mainly Enterobacteriaceae) and a decrease of Bacteroidetes (predominantly Bacteroidaceae). Inclusion of coated sodium butyrate in the diet of chickens per se had no significant effect on caecal microflora of normal healthy chickens but significantly prevented the increase in Firmicute abundance and decrease of Bacteroidetes abundance in E. tenella-infected birds. No significant changes to caecal microflora were observed at the phylum level between control and E. tenella-infected birds given coated sodium butyrate. In conclusion, our results show that coated sodium butyrate can balance the disorders of cecal microflora caused by E. tenella; thus, it can be a useful supplement for the control of avian coccidiosis.
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Affiliation(s)
- Zuoyong Zhou
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Kui Nie
- College of Animal Science and Technology, Southwest University, Beibei District Chongqing, 400715, China
| | - Qingzhou Huang
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Kai Li
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Yingying Sun
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Rongqiong Zhou
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Zhiying Wang
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Shijun Hu
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
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277
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Brauner P, Gromöller S, Pfeifer Y, Wilharm G, Jäckel U. Hatchery workers’ IgG antibody profiles to airborne bacteria. Int J Hyg Environ Health 2017; 220:431-439. [DOI: 10.1016/j.ijheh.2016.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 10/20/2022]
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278
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Costa MC, Bessegatto JA, Alfieri AA, Weese JS, Filho JAB, Oba A. Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken. PLoS One 2017; 12:e0171642. [PMID: 28222110 PMCID: PMC5319738 DOI: 10.1371/journal.pone.0171642] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/24/2017] [Indexed: 11/29/2022] Open
Abstract
Antimicrobials are sometimes given to food animals at low doses in order to promote faster growth. However, the mechanisms by which those drugs improve performance are not fully understood. This study aimed to investigate the impact of zinc bacitracin (55g/ton), enramycin (10g/ton); halquinol® (30g/ton); virginiamycin (16,5g/ton) and avilamycin (10g/ton) on the cecal microbiota of broiler chicken, compared to a control group. Six hundred and twenty four chicks (Cobb 500) arriving to an experimental unit were randomly assigned into each treatment with four repetitions per treatment. The cecal content of 16 animals per treatment (n = 96) was used for DNA extraction and sequencing of the V4 region of the 16S rRNA gene using Illumina technology. The use of antimicrobials induced significant changes in membership but not in structure of the cecal microbiota compared to the control group, suggesting a greater impact on the less abundant species of bacteria present in that environment. Halquinol was the only drug that did not affect microbial membership. Firmicutes comprised the major bacterial phylum present in the cecum of all groups. There was no statistical difference in relative abundances of the main phyla between treated animals and the control group (all P>0.05). Treatment with enramycin was associated with decreased richness and with lower relative abundance of unclassified Firmicutes, Clostridium XI, unclassified Peptostreptococcaceae (all P<0.001) and greater abundance of Clostridium XIVb (P = 0.004) and Anaerosporobacter spp. (P = 0.015), and treatment with bacitracin with greater relative abundance of Bilophila spp. (P = 0.004). Several bacterial genera were identified as representative of usage of each drug. This study used high throughput sequencing to characterize the impact of several antimicrobials in broiler chicken under controlled conditions and add new insights to the current knowledge on how AGPs affect the cecal microbiota of chicken.
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Affiliation(s)
- Marcio C. Costa
- Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
- * E-mail:
| | - Jose A. Bessegatto
- Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Amauri A. Alfieri
- Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - J. Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - João A. B. Filho
- Department of Animal Science, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alexandre Oba
- Department of Animal Science, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
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279
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Best AA, Porter AL, Fraley SM, Fraley GS. Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System. Front Microbiol 2017; 7:2125. [PMID: 28101086 PMCID: PMC5209349 DOI: 10.3389/fmicb.2016.02125] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/16/2016] [Indexed: 02/01/2023] Open
Abstract
Little to no research has been conducted on the gut microbiome of the Pekin duck, yet over 24.5 million ducks are raised for human consumption each year in the United States alone. Knowledge of the microbiome could lead to an understanding of the effects of growing conditions such as the use of prebiotics, probiotics, and enzymes in feeding practices, the use of antibiotics, and the sources of pathogenic bacteria in diseased ducks. In order to characterize changes in the caecal microbiome that occur as ducks develop through a typical industry grow-out period, a 16S rRNA community analysis of caecal contents collected over a 6-week period was conducted using a next generation sequencing approach. Transitions in the composition of the caecal microbiome occurred throughout the lifespan, with a large shift during days 4 through 10 posthatch. Two major phyla of bacteria were found to be present within the caeca of aviary raised ducks, with the relative abundance of each phylum varying by age of the duck. Proteobacteria is dominant for the first 3 days of age, and Firmicutes increases and dominates beginning at day 4. Barn raised ducks contained a significant population of Bacteroidetes in addition to Proteobacteria and Firmicutes at later developmental time points, though this phylum was absent in aviary raised ducks. Genera containing pathogens of anseriformes most often found in industry settings were either absent or found as normal parts of the caecal microbial populations. The high level differences in phylum abundance highlight the importance of well-designed sampling strategies for microbiome based studies. Results showed clear distinctions between Pekin Duck caecal contents and those of Broiler Chickens and Turkey in a qualitative comparison. These data provide a reference point for studies of the Pekin Duck through industry grow-out ages, provide a foundation for understanding the types of bacteria that promote health, and may lead to improved methods to increase yields and decrease instances of disease in agricultural production processes.
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Affiliation(s)
- Aaron A Best
- Department of Biology, Hope College Holland, MI, USA
| | | | - Susan M Fraley
- Department of Biology, Hope CollegeHolland, MI, USA; South Crossing Veterinary CenterCaledonia, MI, USA
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280
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The Bacteriomes of Ileal Mucosa and Cecal Content of Broiler Chickens and Turkeys as Revealed by Metagenomic Analysis. Int J Microbiol 2016; 2016:4320412. [PMID: 28115936 PMCID: PMC5225337 DOI: 10.1155/2016/4320412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/07/2016] [Accepted: 11/27/2016] [Indexed: 12/14/2022] Open
Abstract
The gastrointestinal (GI) bacteriome of poultry is important in host nutrition and health, but its diversity and composition remain poorly characterized. In this study we phylogenetically characterized the bacteriome in the cecal contents and ileal mucosa of chickens and turkeys using metagenomics empowered by pyrosequencing technique. >95% coverage of bacterial diversity was achieved except for the turkey ileal mucosa. Collectively, 3,401 and 125 operational taxonomy units (OTU, defined at a 0.03 phylogenetic distance) in chicken, and 1,687 and 16 OTUs in turkey were identified from the cecal content and the ileal mucosa, respectively. Besides those previously reported, 39 and 50 additional genera of bacteria were identified in the chicken and turkey cecal bacteriome, respectively. Although the GI bacteriomes of the same region in both species exhibited greater similarity than the bacteriomes of different regions within each species, broiler chickens and turkeys harbor a distinct intestinal bacteriome. Such difference may suggest different dietary interventions for bacteriome modulation for enhanced nutrient utilization and gut health. The results may also be useful in developing prebiotics, probiotics, and analytical tools (e.g., phylochips). We also determined the variation in the number of OTUs and variability between two independent pyrosequencing runs and two data processing pipelines.
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281
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Brauner P, Klug K, Jäckel U. Eggshells as a source for occupational exposure to airborne bacteria in hatcheries. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2016; 13:950-959. [PMID: 27341051 DOI: 10.1080/15459624.2016.1200192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Occupational exposure to high concentrations of airborne bacteria in poultry production is related to an increased risk of respiratory disorders. However, potential sources and formation of hatchery bioaerosols are rarely characterized. In this study, bacterial multiplication on fresh shell fragments from turkey hatching eggs under conditions present in a hatcher incubator was investigated. A 105-fold amplification was observed both by colony count and total cell count gaining 4 × 107 cfu/cells per gram eggshell within 30 hr of incubation. Furthermore, the bacterial community present on eggshells was analyzed by generation of 16S rRNA gene clone libraries and identification of eight isolates. RFLP analysis revealed no shift in community composition during incubation and Enterococcus faecalis and Enterococcus gallinarum were found as the predominant species on turkey eggshells, both have been classified as risk group 2 microorganisms (German TRBA 466). Since Enterococcus spp. were found as predominant species on turkey eggshells, contribution of this genus to bioaerosol formation was demonstrated. During different work activities with poult and eggshell handling concentrations of airborne enterococci up to 1.3 × 104 cfu m-3 were detected. In contrast, no enterococci were identified at a day without poult or eggshell processing. In conclusion, turkey hatching eggs carry a viable specific microflora from breeder flocks to hatcheries. After hatching of turkey poults, hatcher incubators and eggshell fragments provide appropriate conditions for excessive bacterial growth. Thus, high bacterial loads on eggshell fragments are a source of potential harmful bioaersols caused by air flows, poult activity, and handling of equipment.
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Affiliation(s)
- Paul Brauner
- a Federal Institute for Occupational Safety and Health , Berlin , Germany
| | - Kerstin Klug
- a Federal Institute for Occupational Safety and Health , Berlin , Germany
| | - Udo Jäckel
- a Federal Institute for Occupational Safety and Health , Berlin , Germany
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282
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Awad WA, Mann E, Dzieciol M, Hess C, Schmitz-Esser S, Wagner M, Hess M. Age-Related Differences in the Luminal and Mucosa-Associated Gut Microbiome of Broiler Chickens and Shifts Associated with Campylobacter jejuni Infection. Front Cell Infect Microbiol 2016; 6:154. [PMID: 27921008 PMCID: PMC5118433 DOI: 10.3389/fcimb.2016.00154] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/01/2016] [Indexed: 02/01/2023] Open
Abstract
Despite the importance of gut microbiota for broiler performance and health little is known about the composition of this ecosystem, its development and response towards bacterial infections. Therefore, the current study was conducted to address the composition and structure of the microbial community in broiler chickens in a longitudinal study from day 1 to day 28 of age in the gut content and on the mucosa. Additionally, the consequences of a Campylobacter (C.) jejuni infection on the microbial community were assessed. The composition of the gut microbiota was analyzed with 16S rRNA gene targeted Illumina MiSeq sequencing. Sequencing of 130 samples yielded 51,825,306 quality-controlled sequences, which clustered into 8285 operational taxonomic units (OTUs; 0.03 distance level) representing 24 phyla. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Tenericutes were the main components of the gut microbiota, with Proteobacteria and Firmicutes being the most abundant phyla (between 95.0 and 99.7% of all sequences) at all gut sites. Microbial communities changed in an age-dependent manner. Whereas, young birds had more Proteobacteria, Firmicutes, and Tenericutes dominated in older birds (>14 days old). In addition, 28 day old birds had more diverse bacterial communities than young birds. Furthermore, numerous significant differences in microbial profiles between the mucosa and luminal content of the small and large intestine were detected, with some species being strongly associated with the mucosa whereas others remained within the luminal content of the gut. Following oral infection of 14 day old broiler chickens with 1 × 108 CFU of C. jejuni NCTC 12744, it was found that C. jejuni heavily colonized throughout the small and large intestine. Moreover, C. jejuni colonization was associated with an alteration of the gut microbiota with infected birds having a significantly lower abundance of Escherichia (E.) coli at different gut sites. On the contrary, the level of Clostridium spp. was higher in infected birds compared with birds from the negative controls. In conclusion, the obtained results demonstrate how the bacterial microbiome composition changed within the early life of broiler chickens in the gut lumen and on the mucosal surface. Furthermore, our findings confirmed that the Campylobacter carrier state in chicken is characterized by multiple changes in the intestinal ecology within the host.
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Affiliation(s)
- Wageha A Awad
- Department for Farm Animals and Veterinary Public Health, Clinic for Poultry and Fish Medicine, University of Veterinary MedicineVienna, Austria; Department of Animal Hygiene, Poultry and Environment, Faculty of Veterinary Medicine, South Valley UniversityQena, Egypt
| | - Evelyne Mann
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, University of Veterinary Medicine Vienna, Austria
| | - Monika Dzieciol
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, University of Veterinary Medicine Vienna, Austria
| | - Claudia Hess
- Department for Farm Animals and Veterinary Public Health, Clinic for Poultry and Fish Medicine, University of Veterinary Medicine Vienna, Austria
| | - Stephan Schmitz-Esser
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, University of Veterinary Medicine Vienna, Austria
| | - Martin Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, University of Veterinary Medicine Vienna, Austria
| | - Michael Hess
- Department for Farm Animals and Veterinary Public Health, Clinic for Poultry and Fish Medicine, University of Veterinary Medicine Vienna, Austria
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283
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Xu Y, Yang H, Zhang L, Su Y, Shi D, Xiao H, Tian Y. High-throughput sequencing technology to reveal the composition and function of cecal microbiota in Dagu chicken. BMC Microbiol 2016; 16:259. [PMID: 27814685 PMCID: PMC5097418 DOI: 10.1186/s12866-016-0877-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 10/28/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. The coding capacity of microbiome vastly surpasses that of the host's genome, encoding biochemical pathways that the host has not developed. An optimal gut microbiota can increase agricultural productivity. This study aims to explore the composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range (outdoor, OD) and cage (indoor, ID) raising. RESULTS Cecal samples were collected from 24 chickens across 4 groups (12-w OD, 12-w ID, 18-w OD, and 18-w ID). We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions to characterize the cecal microbiota of Dagu chicken and compare the difference of cecal microbiota between free-range and cage raising chickens. It was found that 34 special operational taxonomic units (OTUs) in OD groups and 4 special OTUs in ID groups. 24 phyla were shared by the 24 samples. Bacteroidetes was the most abundant phylum with the largest proportion, followed by Firmicutes and Proteobacteria. The OD groups showed a higher proportion of Bacteroidetes (>50 %) in cecum, but a lower Firmicutes/Bacteroidetes ratio in both 12-w old (0.42, 0.62) and 18-w old groups (0.37, 0.49) compared with the ID groups. Cecal microbiota in the OD groups have higher abundance of functions involved in amino acids and glycan metabolic pathway. CONCLUSION The composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range and cage raising are different. The cage raising mode showed a lower proportion of Bacteroidetes in cecum, but a higher Firmicutes/Bacteroidetes ratio compared with free-range mode. Cecal microbiota in free-range mode have higher abundance of functions involved in amino acids and glycan metabolic pathway.
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Affiliation(s)
- Yunhe Xu
- Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China
| | - Huixin Yang
- Department of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lili Zhang
- Department of Food Science, Liaoning Medical University, Jinzhou, Liaoning, China
| | - Yuhong Su
- Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China
| | - Donghui Shi
- Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China
| | - Haidi Xiao
- Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China
| | - Yumin Tian
- Department of Animal Husbandry & Veterinary Medicine, Liaoning Medical University, Jinzhou, Liaoning, 121000, China.
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284
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Wang J, Fan H, Han Y, Wei J, Zhao J, Zhou Z. Pyrosequencing of the broiler chicken gastrointestinal tract reveals the regional similarity and dissimilarity of microbial community. CANADIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1139/cjas-2015-0120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jin Wang
- School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, P.O. Box 300072, Tianjin, People’s Republic of China
| | - Huan Fan
- Tianjin Institute of Animal Husbandry and Veterinary Research, 17 kilometres, Jinjing Road, Xiqing District, P.O. Box 300384, Tianjin, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, 92 Weijin Road, Nankai District, P.O. Box 300072, Tianjin, People’s Republic of China
| | - Ye Han
- School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, P.O. Box 300072, Tianjin, People’s Republic of China
| | - Jiping Wei
- School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, P.O. Box 300072, Tianjin, People’s Republic of China
| | - Jinzhao Zhao
- Tianjin Kuntai Environment & Energy Science and Technology Development Co., Ltd., 31 Fukang Road, Nankai District, P.O. Box 300191, Tianjin, People’s Republic of China
| | - Zhijiang Zhou
- School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, P.O. Box 300072, Tianjin, People’s Republic of China
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285
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Dunlop MW, Blackall PJ, Stuetz RM. Odour emissions from poultry litter - A review litter properties, odour formation and odorant emissions from porous materials. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 177:306-319. [PMID: 27111649 DOI: 10.1016/j.jenvman.2016.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/21/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Odour emissions from meat chicken sheds can at times cause odour impacts on surrounding communities. Litter is seen as the primary source of this odour. Formation and emission of odour from meat chicken litter during the grow-out period are influenced by various factors such as litter conditions, the environment, microbial activity, properties of the odorous gases and management practices. Odour emissions vary spatially and temporally. This variability has made it challenging to understand how specific litter conditions contribute to odour emissions from the litter and production sheds. Existing knowledge on odorants, odour formation mechanisms and emission processes that contribute to odour emissions from litter are reviewed. Litter moisture content and water thermodynamics (i.e. water activity, Aw) are also examined as factors that contribute to microbial odour formation, physical litter conditions and the exchange of individual odorant gases at the air-water interface. Substantial opportunities exist for future research on litter conditions and litter formation mechanisms and how these contribute to odour emissions. Closing this knowledge gap will improve management strategies that intercept and interfere with odour formation and emission processes leading to an overall reduction in the potential to cause community impacts.
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Affiliation(s)
- Mark W Dunlop
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, Qld 4350, Australia; University of New South Wales, School of Civil and Environmental Engineering, Sydney, NSW 2052, Australia; Poultry CRC, PO Box U242, University of New England, Armidale, NSW 2351, Australia.
| | - Patrick J Blackall
- Poultry CRC, PO Box U242, University of New England, Armidale, NSW 2351, Australia; The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Brisbane 4067, Australia
| | - Richard M Stuetz
- University of New South Wales, School of Civil and Environmental Engineering, Sydney, NSW 2052, Australia
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286
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Wang L, Lilburn M, Yu Z. Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens. Front Microbiol 2016; 7:593. [PMID: 27242676 PMCID: PMC4870231 DOI: 10.3389/fmicb.2016.00593] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022] Open
Abstract
Poultry litter is a mixture of bedding materials and enteric bacteria excreted by chickens, and it is typically reused for multiple growth cycles in commercial broiler production. Thus, bacteria can be transmitted from one growth cycle to the next via litter. However, it remains poorly understood how litter reuse affects development and composition of chicken gut microbiota. In this study, the effect of litter reuse on the microbiota in litter and in chicken gut was investigated using 2 litter management regimens: fresh vs. reused litter. Samples of ileal mucosa and cecal digesta were collected from young chicks (10 days of age) and mature birds (35 days of age). Based on analysis using DGGE and pyrosequencing of bacterial 16S rRNA gene amplicons, the microbiota of both the ileal mucosa and the cecal contents was affected by both litter management regimen and age of birds. Faecalibacterium, Oscillospira, Butyricicoccus, and one unclassified candidate genus closely related to Ruminococcus were most predominant in the cecal samples, while Lactobacillus was predominant in the ileal samples at both ages and in the cecal samples collected at day 10. At days 10 and 35, 8 and 3 genera, respectively, in the cecal luminal microbiota differed significantly in relative abundance between the 2 litter management regimens. Compared to the fresh litter, reused litter increased predominance of halotolerant/alkaliphilic bacteria and Faecalibacterium prausnitzii, a butyrate-producing gut bacterium. This study suggests that litter management regimens affect the chicken GI microbiota, which may impact the host nutritional status and intestinal health.
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Affiliation(s)
- Lingling Wang
- Department of Animal Sciences, The Ohio State University Columbus, OH, USA
| | - Mike Lilburn
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA; Department of Animal Sciences, Ohio Agriculture Research and Development CenterWooster, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA; Department of Animal Sciences, Ohio Agriculture Research and Development CenterWooster, OH, USA
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287
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An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers. Sci Rep 2016; 6:25882. [PMID: 27174843 PMCID: PMC4865835 DOI: 10.1038/srep25882] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/21/2016] [Indexed: 12/15/2022] Open
Abstract
Bacterial chondronecrosis with osteomyelitis (BCO) is a common cause of lameness in commercial broiler chickens worldwide. BCO represents substantial production loss and welfare issues of chickens. The bacterial species or communities underlying BCO pathogenesis still remain to be fully characterized. To gain insights on blood microbiota in broilers and its potential association with BCO, blood samples collected from healthy (n = 240) and lame (n = 12) chickens were analyzed by deep sequencing of 16S RNA genes. The chicken blood microbiota were dominated by Proteobacteria (60.58% ± 0.65) followed by Bactroidetes (13.99% ± 0.29), Firmicutes (11.45% ± 0.51), Actinobacteria (10.21% ± 0.37) and Cyanobacteria (1.96% ± 0.21) that constituted 98.18% (± 0.22) of the whole phyla. The bacterial communities consist of 30–40 OTUs in the blood of broiler chickens, regardless of ages and other environmental or host conditions, and the blood microbiomes of BCO chickens were largely distinct from those of healthy chickens. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) method revealed that Staphylococcus, Granulicatella, and Microbacterium were significantly enriched in BCO chickens as compared to healthy chickens. The results from this study have significant implications in understanding blood microbiota present in broiler chickens and its potential role in BCO pathogenesis.
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288
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Bacterial Succession in the Broiler Gastrointestinal Tract. Appl Environ Microbiol 2016; 82:2399-2410. [PMID: 26873323 DOI: 10.1128/aem.02549-15] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/06/2016] [Indexed: 01/13/2023] Open
Abstract
A feeding trial was performed with broilers receiving a diet of wheat-based feed (WBF), maize-based feed (MBF), or maize-based concentrates supplemented with 15% or 30% crimped kernel maize silage (CKMS-15 or CKMS-30, respectively). The aim of the study was to investigate the bacterial community compositions of the crop, gizzard, ileum, and cecum contents in relation to the feeding strategy and age (8, 15, 22, 25, 29, or 36 days). Among the four dietary treatments, bacterial diversity was analyzed for MBF and CKMS-30 by 454 pyrosequencing of the 16S rRNA gene. Since the diets had no significant influence on bacterial diversity, data were pooled for downstream analysis. With increasing age, a clear succession of bacterial communities and increased bacterial diversity were observed.Lactobacillaceae(belonging mainly to the genus Lactobacillus) represented most of the Firmicutesat all ages and in all segments of the gut except the cecum. The development of a "mature" microbiota in broilers occurred during the period from days 15 to 22. Striking increases in the relative abundances of Lactobacillus salivarius(17 to 36%) and clostridia (11 to 18%), and a concomitant decrease in the relative abundance of Lactobacillus reuteri, were found in the ileum after day 15. The concentration of deconjugated bile salts increased in association with the increased populations of L. salivarius and clostridia. Both L. salivarius and clostridia deconjugate bile acids, and increases in the abundances of these bacteria might be associated with growth reduction and gastrointestinal (GI) disorders occurring in the critical period of broiler life between days 20 and 30.
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289
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Hutsko SL, Meizlisch K, Wick M, Lilburn MS. Early intestinal development and mucin transcription in the young poult with probiotic and mannan oligosaccharide prebiotic supplementation. Poult Sci 2016; 95:1173-8. [PMID: 26944966 DOI: 10.3382/ps/pew019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/05/2016] [Indexed: 01/05/2023] Open
Abstract
Alternative and adjunctive approaches to decreasing the use of dietary antibiotics are becoming popular areas of study. Supplemental probiotics (commensal microbes) and prebiotics (indigestible complex carbohydrates) are 2 dietary approaches to facilitating the intestinal colonization of beneficial bacteria to compete with potential pathogens, thus creating a healthy mucosal environment. The intestinal mucosa is composed of mucin glycoproteins, which play a key role in preventing the attachment of pathogenic bacteria. At hatch, the neonatal turkey intestine is relatively aseptic and vulnderable to bacterial colonization by both commensal and pathogenic microbes. In the current study, we determined the transcription of MUC2, the primary mucin protein produced by goblet cells within the small intestine, and we also measured intestinal morphology immediately post-hatch through d 11. Poults were fed a conventional starter diet, the starter diet supplemented with one of 2 commercial probiotics (A, B), or a commercial mannan oligosaccharide. MUC2 transcription increased from d zero to d 4 post-hatch (P< 0.05), but there was no effect of probiotic or prebiotic supplementation. Villus height and villus area both increased with Probiotic B and mannan oligosaccharide supplementation (P<0.05) and there was a significant d X treatment interaction effect for crypt depth (P=0.007). These results suggest that probiotic and prebiotic supplementation can positively alter the intestinal microenvironment.
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Affiliation(s)
- S L Hutsko
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - K Meizlisch
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - M Wick
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - M S Lilburn
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
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290
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Oakley BB, Kogut MH. Spatial and Temporal Changes in the Broiler Chicken Cecal and Fecal Microbiomes and Correlations of Bacterial Taxa with Cytokine Gene Expression. Front Vet Sci 2016; 3:11. [PMID: 26925404 PMCID: PMC4759570 DOI: 10.3389/fvets.2016.00011] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/04/2016] [Indexed: 12/31/2022] Open
Abstract
To better understand the ecology of the poultry gastrointestinal (GI) microbiome and its interactions with the host, we compared GI bacterial communities by sample type (fecal or cecal), time (1, 3, and 6 weeks posthatch), and experimental pen (1, 2, 3, or 4), and measured cecal mRNA transcription of the cytokines IL18, IL1β, and IL6, IL10, and TGF-β4. The microbiome was characterized by sequencing of 16S rRNA gene amplicons, and cytokine gene expression was measured by a panel of quantitative-PCR assays targeting mRNAs. Significant differences were observed in the microbiome by GI location (fecal versus cecal) and bird age as determined by permutational MANOVA and UniFrac phylogenetic hypothesis tests. At 1-week posthatch, bacterial genera significantly over-represented in fecal versus cecal samples included Gallibacterium and Lactobacillus, while the genus Bacteroides was significantly more abundant in the cecum. By 6-week posthatch, Clostridium and Caloramator (also a Clostridiales) sequence types had increased significantly in the cecum and Lactobacillus remained over-represented in fecal samples. In the ceca, the relative abundance of sequences classified as Clostridium increased by ca. 10-fold each sampling period from 0.1% at 1 week to 1% at 3 week and 18% at 6 week. Increasing community complexity through time were observed in increased taxonomic richness and diversity. IL18 and IL1β significantly (p < 0.05, pairwise t-tests) increased to maximum mean expression levels 1.5 fold greater at week 3 than 1, while IL6 significantly decreased to 0.8- and 0.5-fold expression at 3- and 6-week posthatch, respectively relative to week 1. Transcription of pro-inflammatory cytokines was generally negatively correlated with the relative abundance of various members of the phylum Firmicutes and positively correlated with Proteobacteria. Correlations of the microbiome with specific cytokine mRNA transcription highlight the importance of the GI microbiome for bird health and productivity and may be a successful high-throughput strategy to identify bacterial taxa with specific immune-modulatory properties.
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Affiliation(s)
- Brian B Oakley
- College of Veterinary Medicine, Western University of Health Sciences , Pomona, CA , USA
| | - Michael H Kogut
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Area Research Center , College Station, TX , USA
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291
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Gómez-Doñate M, Casanovas-Massana A, Muniesa M, Blanch AR. Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water. Microbiologyopen 2016; 5:83-94. [PMID: 26763626 PMCID: PMC4767429 DOI: 10.1002/mbo3.313] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/06/2015] [Accepted: 10/13/2015] [Indexed: 12/15/2022] Open
Abstract
Bacteroides spp. have been proposed as indicators of fecal contamination in microbial source tracking (MST) methodologies. The aim of this study was to develop new qPCR assays that target host‐specific Bacteroidal 16S ribosomal RNA genes, to determine the source of fecal contamination in water. Denaturing gradient gel electrophoresis (DGGE) was used to select for host‐specific bands of Bacteroides associated with a fecal pollution source and later to design four qPCR host‐specific assays. A set of common primers for Bacteroides spp., four different Bacteroides spp. host‐associated hydrolysis probes (human, cattle, pig, and poultry), and one hydrolysis probe for the Bacteroides genus were designed. This set of qPCR assays together with other previously developed Bacteroidetes MST targets were used to analyze water samples with fecal contamination from the four sources studied. The host‐specific Bacteroides qPCRs designed for human (HMprobeBac), pig (PGprobeBac), and poultry (PLprobeBac) were highly specific for its sources (1.0, 0.97, and 1.0, respectively) although its sensitivity was lower (0.45, 0.50, and 0.73, respectively). The cattle‐specific qPCR was totally unspecific and was discarded for future experiments. When compared to previously designed assays, the human and pig qPCRs showed better accuracies (0.86 and 0.84) than their counterparts HF183 and Pig‐2‐Bac (0.38 and 0.65). Thus, the newly designed human, pig, and poultry qPCR assays outperform other methods developed until date and may be useful for source tracking purposes.
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Affiliation(s)
- Marta Gómez-Doñate
- Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, Catalonia, 08028, Spain
| | - Arnau Casanovas-Massana
- Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, Catalonia, 08028, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, Catalonia, 08028, Spain
| | - Anicet R Blanch
- Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, Catalonia, 08028, Spain
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292
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Buntyn JO, Schmidt TB, Nisbet DJ, Callaway TR. The Role of Direct-Fed Microbials in Conventional Livestock Production. Annu Rev Anim Biosci 2015; 4:335-55. [PMID: 26667362 DOI: 10.1146/annurev-animal-022114-111123] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Supplementation of direct-fed microbials (DFM) as a means to improve the health and performance of livestock has generated significant interest over the past 15+ years. A driving force for this increased interest in DFM is to reduce or eliminate the use of low-dose antibiotics in livestock production. This increased attention toward DFM supplementation has generated an extensive body of research. This effort has resulted in conflicting reports. Although there has been considerable variation in the design of these studies, one of the main causes for this lack of consistency may be attributed to the variation in the experimental immune challenge incorporated to evaluate DFM supplementation. Taking into account the experimental immune challenge, there is strong evidence to suggest that DFM supplementation may have an impact on the immune response, overall health, and performance of livestock.
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Affiliation(s)
- J O Buntyn
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska 68583; ,
| | - T B Schmidt
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska 68583; ,
| | - D J Nisbet
- Food and Feed Safety Research Unit, South Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, Texas 77845;
| | - T R Callaway
- Food and Feed Safety Research Unit, South Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, Texas 77845;
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293
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Reed S, Neuman H, Moscovich S, Glahn RP, Koren O, Tako E. Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function. Nutrients 2015; 7:9768-84. [PMID: 26633470 PMCID: PMC4690049 DOI: 10.3390/nu7125497] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 02/06/2023] Open
Abstract
Zinc (Zn) deficiency is a prevalent micronutrient insufficiency. Although the gut is a vital organ for Zn utilization, and Zn deficiency is associated with impaired intestinal permeability and a global decrease in gastrointestinal health, alterations in the gut microbial ecology of the host under conditions of Zn deficiency have yet to be studied. Using the broiler chicken (Gallus gallus) model, the aim of this study was to characterize distinct cecal microbiota shifts induced by chronic dietary Zn depletion. We demonstrate that Zn deficiency induces significant taxonomic alterations and decreases overall species richness and diversity, establishing a microbial profile resembling that of various other pathological states. Through metagenomic analysis, we show that predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways responsible for macro- and micronutrient uptake are significantly depleted under Zn deficiency; along with concomitant decreases in beneficial short chain fatty acids, such depletions may further preclude optimal host Zn availability. We also identify several candidate microbes that may play a significant role in modulating the bioavailability and utilization of dietary Zn during prolonged deficiency. Our results are the first to characterize a unique and dysbiotic cecal microbiota during Zn deficiency, and provide evidence for such microbial perturbations as potential effectors of the Zn deficient phenotype.
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Affiliation(s)
- Spenser Reed
- USDA-ARS Robert Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
- College of Medicine, the University of Arizona, Tucson, AZ 85724, USA.
| | - Hadar Neuman
- Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, Safed 1311502, Israel.
| | - Sharon Moscovich
- Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, Safed 1311502, Israel.
| | - Raymond P Glahn
- USDA-ARS Robert Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
| | - Omry Koren
- Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, Safed 1311502, Israel.
| | - Elad Tako
- USDA-ARS Robert Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
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294
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Witzig M, Camarinha da Silva A, Green-Engert R, Hoelzle K, Zeller E, Seifert J, Hoelzle LE, Rodehutscord M. Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing. PLoS One 2015; 10:e0143442. [PMID: 26588075 PMCID: PMC4654470 DOI: 10.1371/journal.pone.0143442] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/04/2015] [Indexed: 12/02/2022] Open
Abstract
Molecular fingerprinting and sequencing based techniques have been widely used to characterize microbial communities. Terminal restriction fragment length polymorphism (T-RFLP) and 454-pyrosequencing were used to determine the microorganisms present in the different sections of the chicken gastrointestinal tract (GIT) (crop, jejunum, ileum and caeca). Broilers fed with diets differing in phosphorous (P) and calcium (Ca) as well as in phytase levels were used to study the microbiota of the upper and lower part of the GIT. A database with terminal restriction fragments (T-RF) of the most important organism present in the different gastrointestinal sections was constructed. The analysis revealed a distinct microbial assemblage on each section. Regardless of the diet, crop, jejunum and ileum were mainly colonized by Lactobacillaceae, and caeca were the most diverse site. The correlation between Lactobacillus crispatus and L. reuteri was positive in the crop, but negative in the jejunum. In crop samples, higher P and Ca levels led to a shift in the abundance of L. reuteri and L. crispatus to L. salivarius and L. taiwanensis whereas in the ileum supplementation of phytase favored L. salivarius and L. taiwanensis but resulted in decreased abundance of L. crispatus. Both methods were correlating significantly, being T-RFLP a reliable fingerprinting method to rapidly analyze large numbers of samples in a cost-effective and rapid manner. Results are easy to interpret with no need of deep bioinformatics knowledge and can be integrated with taxonomic information.
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Affiliation(s)
- Maren Witzig
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
- * E-mail:
| | | | | | - Katharina Hoelzle
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
| | - Ellen Zeller
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
| | - Jana Seifert
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
| | - Ludwig E. Hoelzle
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
| | - Markus Rodehutscord
- Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany
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295
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Neumann AP, Suen G. Differences in major bacterial populations in the intestines of mature broilers after feeding virginiamycin or bacitracin methylene disalicylate. J Appl Microbiol 2015; 119:1515-26. [PMID: 26425940 DOI: 10.1111/jam.12960] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 11/27/2022]
Abstract
AIMS The purpose of this study was to compare the effects of feeding virginiamycin or bacitracin methylene disalicylate (BMD), two in-feed antibiotics typically used by commercial poultry producers in the United States, on the chicken gastrointestinal microbiota. METHODS AND RESULTS 454 pyrosequencing of the V6-V8 region of the 16S rRNA gene and quantitative PCR were employed to examine the bacterial microbiota and Clostridium perfringens, respectively, in the jejunum and caecum of market-age broiler chickens over four replicate grow-outs. CONCLUSIONS Our results suggest that virginiamycin has a more pronounced impact on broiler gastrointestinal tract bacterial communities, relative to BMD, manifested primarily through significant enrichments in the genus Faecalibacterium in the caecum and a distinct population of Lactobacillus, OTU_02, in both the jejunum and caecum. No evidence for a difference among the diets in Cl. perfringens levels in the jejunum or caecum was observed. SIGNIFICANCE AND IMPACT OF THE STUDY This work represents the highest resolution comparison to date of the jejunum and caecum microbiota in broilers fed either virginiamycin or BMD, and provides evidence for specific bacterial OTUs potentially involved in the health and performance benefits typically attributed to these in-feed antibiotics.
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Affiliation(s)
- A P Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - G Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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296
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Płowiec A, Sławińska A, Siwek MZ, Bednarczyk MF. Effect of in ovo administration of inulin andLactococcus lactison immune-related gene expression in broiler chickens. Am J Vet Res 2015; 76:975-82. [DOI: 10.2460/ajvr.76.11.975] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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297
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Jones RT, Borchert J, Eisen R, MacMillan K, Boegler K, Gage KL. Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda. PLoS One 2015; 10:e0141057. [PMID: 26485147 PMCID: PMC4617453 DOI: 10.1371/journal.pone.0141057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/01/2015] [Indexed: 11/19/2022] Open
Abstract
The vast majority of human plague cases currently occur in sub-Saharan Africa. The primary route of transmission of Yersinia pestis, the causative agent of plague, is via flea bites. Non-pathogenic flea-associated bacteria may interact with Y. pestis within fleas and it is important to understand what factors govern flea-associated bacterial assemblages. Six species of fleas were collected from nine rodent species from ten Ugandan villages between October 2010 and March 2011. A total of 660,345 16S rRNA gene DNA sequences were used to characterize bacterial communities of 332 individual fleas. The DNA sequences were binned into 421 Operational Taxonomic Units (OTUs) based on 97% sequence similarity. We used beta diversity metrics to assess the effects of flea species, flea sex, rodent host species, site (i.e. village), collection date, elevation, mean annual precipitation, average monthly precipitation, and average monthly temperature on bacterial community structure. Flea species had the greatest effect on bacterial community structure with each flea species harboring unique bacterial lineages. The site (i.e. village), rodent host, flea sex, elevation, precipitation, and temperature also significantly affected bacterial community composition. Some bacterial lineages were widespread among flea species (e.g. Bartonella spp. and Wolbachia spp.), but each flea species also harbored unique bacterial lineages. Some of these lineages are not closely related to known bacterial diversity and likely represent newly discovered lineages of insect symbionts. Our finding that flea species has the greatest effect on bacterial community composition may help future investigations between Yersinia pestis and non-pathogenic flea-associated bacteria. Characterizing bacterial communities of fleas during a plague epizootic event in the future would be helpful.
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Affiliation(s)
- Ryan Thomas Jones
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
- Montana Institute on Ecosystems, Montana State University, Bozeman, Montana, United States of America
| | - Jeff Borchert
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Rebecca Eisen
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Katherine MacMillan
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Karen Boegler
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Kenneth L. Gage
- Division of Vector-Borne Disease; Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
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298
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Bortoluzzi C, Menten J, Pereira R, Fagundes N, Napty G, Pedroso A, Bigaton A, Andreote F. Hops β-acids and zinc bacitracin affect the performance and intestinal microbiota of broilers challenged with Eimeria acervulina and Eimeria tenella. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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299
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Thibodeau A, Fravalo P, Yergeau É, Arsenault J, Lahaye L, Letellier A. Chicken Caecal Microbiome Modifications Induced by Campylobacter jejuni Colonization and by a Non-Antibiotic Feed Additive. PLoS One 2015; 10:e0131978. [PMID: 26161743 PMCID: PMC4498643 DOI: 10.1371/journal.pone.0131978] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 01/19/2023] Open
Abstract
Campylobacter jejuni is an important zoonotic foodborne pathogen causing acute gastroenteritis in humans. Chickens are often colonized at very high numbers by C. jejuni, up to 10(9) CFU per gram of caecal content, with no detrimental effects on their health. Farm control strategies are being developed to lower the C. jejuni contamination of chicken food products in an effort to reduce human campylobacteriosis incidence. It is believed that intestinal microbiome composition may affect gut colonization by such undesirable bacteria but, although the chicken microbiome is being increasingly characterized, information is lacking on the factors affecting its modulation, especially by foodborne pathogens. This study monitored the effects of C. jejuni chicken caecal colonization on the chicken microbiome in healthy chickens. It also evaluated the capacity of a feed additive to affect caecal bacterial populations and to lower C. jejuni colonization. From day-0, chickens received or not a microencapsulated feed additive and were inoculated or not with C. jejuni at 14 days of age. Fresh caecal content was harvested at 35 days of age. The caecal microbiome was characterized by real time quantitative PCR and Ion Torrent sequencing. We observed that the feed additive lowered C. jejuni caecal count by 0.7 log (p<0.05). Alpha-diversity of the caecal microbiome was not affected by C. jejuni colonization or by the feed additive. C. jejuni colonization modified the caecal beta-diversity while the feed additive did not. We observed that C. jejuni colonization was associated with an increase of Bifidobacterium and affected Clostridia and Mollicutes relative abundances. The feed additive was associated with a lower Streptococcus relative abundance. The caecal microbiome remained relatively unchanged despite high C. jejuni colonization. The feed additive was efficient in lowering C. jejuni colonization while not disturbing the caecal microbiome.
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Affiliation(s)
- Alexandre Thibodeau
- NSERC Industrial Research Chair in Meat-Safety (CRSV), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Swine and Avian Infectious Disease Research Centre (CRIPA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Groupe de recherche et d’enseignement en salubrité alimentaire (GRESA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- * E-mail: (AT); (AL)
| | - Philippe Fravalo
- NSERC Industrial Research Chair in Meat-Safety (CRSV), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Swine and Avian Infectious Disease Research Centre (CRIPA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Groupe de recherche et d’enseignement en salubrité alimentaire (GRESA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
| | - Étienne Yergeau
- National Research Council of Canada, Montréal, Québec, Canada
| | - Julie Arsenault
- Swine and Avian Infectious Disease Research Centre (CRIPA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Groupe de recherche et d’enseignement en salubrité alimentaire (GRESA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
| | | | - Ann Letellier
- NSERC Industrial Research Chair in Meat-Safety (CRSV), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Swine and Avian Infectious Disease Research Centre (CRIPA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- Groupe de recherche et d’enseignement en salubrité alimentaire (GRESA), Université de Montréal, Faculty of Veterinary Medicine, Saint-Hyacinthe, Québec, Canada
- * E-mail: (AT); (AL)
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Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol 2015; 6:673. [PMID: 26191057 PMCID: PMC4490257 DOI: 10.3389/fmicb.2015.00673] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/19/2015] [Indexed: 01/16/2023] Open
Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.
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Affiliation(s)
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of AucklandAuckland, New Zealand
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