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Joat N, Bajagai YS, Van TTH, Stanley D, Chousalkar K, Moore RJ. The temporal fluctuations and development of faecal microbiota in commercial layer flocks. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 15:197-209. [PMID: 38023383 PMCID: PMC10679818 DOI: 10.1016/j.aninu.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/02/2023] [Accepted: 07/28/2023] [Indexed: 12/01/2023]
Abstract
The microbiota of the gastrointestinal tract influences gut health, which in turn strongly impacts the general health and productivity of laying hens. It is essential to characterise the composition and temporal development of the gut microbiota in healthy layers raised under different management systems, to understand the variations in typical healthy microbiota structure, so that deviations from this might be recognised and correlated with production and health issues when they arise. The present investigation aimed to study the temporal development and phylogenetic composition of the gut microbiota of four commercially raised layer flocks from hatch to end of the production cycle. Non-intrusive faecal sampling was undertaken as a proxy to represent the gut microbiota. Sequencing of 16S rRNA gene amplicons was used to characterise the microbiota. Beta diversity analysis indicated that each faecal microbiota was different across the four flocks and had subtly different temporal development patterns. Despite these inter-flock differences, common patterns of microbiota development were identified. Firmicutes and Proteobacteria were dominant at an early age in all flocks. The microbiota developed gradually during the rearing phase; richness and diversity increased after 42 d of age and then underwent significant changes in composition after the shift to the production farms, with Bacteroidota becoming more dominant in older birds. By developing a more profound knowledge of normal microbiota development in layers, opportunities to harness the microbiota to aid in the management of layer gut health and productivity may be more clearly seen and realised.
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Affiliation(s)
- Nitish Joat
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Yadav S. Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4701, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria, 3083, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Queensland, 4701, Australia
| | - Kapil Chousalkar
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Robert J. Moore
- School of Science, RMIT University, Bundoora, Victoria, 3083, Australia
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2
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Yan Y, Zhang J, Chen X, Wang Z. Effects of Black Soldier Fly Larvae ( Hermetia illucens Larvae) Meal on the Production Performance and Cecal Microbiota of Hens. Vet Sci 2023; 10:vetsci10050364. [PMID: 37235447 DOI: 10.3390/vetsci10050364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The effects of Hermetia illucens larvae meal (HILM) as a feed supplement on production performance and cecal microflora were studied in 900 Hy-line Brown laying hens. Laying hens (60 weeks old) were randomly divided into four groups. Each group had five replicates, and each replicate had 45 hens. The control group was fed with a corn-soybean-based diet, and the experimental groups were fed with 1% HILM, 2% HILM, or 3% HILM. Results were as follows: (1) With the increase in HILM level, the laying rate increased linearly (p ≤ 0.05), and the feed/egg and cracked-egg rate decreased linearly (p ≤ 0.05). (2) Community composition analysis showed that the dominant bacteria in each group were Bacteroidetes and Firmicutes, followed by Actinobacteria and Proteobacteria, which accounted for more than 97% of 16S rRNA gene sequence of the total cecal bacteria. (3) Alpha diversity analysis at the operational taxonomic unit classification level showed that the HILM-addition groups had higher community richness and community diversity than the control group. (4) Principal co-ordinates analysis showed that the cecum samples in each group were significantly separated (p ≤ 0.05). At the phylum level, the relative abundance of Bacteroidetes in the HILM addition groups was significantly lower than that in the control group (p < 0.001), and the relative abundance of Firmicutes in the HILM addition groups was significantly higher than that in the control group (p < 0.001). In conclusion, dietary HILM supplementation had a significant effect on the production performance and cecal microflora of laying hens at the late laying period under the conditions of this experiment but had no adverse effect on the intestinal dominant flora.
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Affiliation(s)
- Yan Yan
- Henan Provincial Academician Workstation of Feed Resource Development and Healthy Livestock, Department of Animal Science and Technology, Henan University of Science and Technology, Luoyang 271023, China
| | - Jinjin Zhang
- Henan Provincial Academician Workstation of Feed Resource Development and Healthy Livestock, Department of Animal Science and Technology, Henan University of Science and Technology, Luoyang 271023, China
| | - Xiaochen Chen
- Henan Provincial Academician Workstation of Feed Resource Development and Healthy Livestock, Department of Animal Science and Technology, Henan University of Science and Technology, Luoyang 271023, China
| | - Zhanbin Wang
- Henan Provincial Academician Workstation of Feed Resource Development and Healthy Livestock, Department of Animal Science and Technology, Henan University of Science and Technology, Luoyang 271023, China
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3
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Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep 2023; 13:4488. [PMID: 36934111 PMCID: PMC10024708 DOI: 10.1038/s41598-023-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 03/20/2023] Open
Abstract
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
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Affiliation(s)
- Ji Eun Kim
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hein M Tun
- School of Public Health, Li Ka Shing, Faculty of Medicine, HKU-Pasteur Research Pole, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Animal Science Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kimberly M Cheng
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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Zhen W, Liu Y, Shao Y, Ma Y, Wu Y, Guo F, Abbas W, Guo Y, Wang Z. Yeast β-Glucan Altered Intestinal Microbiome and Metabolome in Older Hens. Front Microbiol 2022; 12:766878. [PMID: 34975793 PMCID: PMC8718749 DOI: 10.3389/fmicb.2021.766878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 12/31/2022] Open
Abstract
The prebiotics- and probiotics-mediated positive modulation of the gut microbiota composition is considered a useful approach to improve gut health and food safety in chickens. This study explored the effects of yeast β-glucan (YG) supplementation on intestinal microbiome and metabolites profiles as well as mucosal immunity in older hens. A total of 256 43-week-old hens were randomly assigned to two treatments, with 0 and 200 mg/kg of YG. Results revealed YG-induced downregulation of toll-like receptors (TLRs) and cytokine gene expression in the ileum without any effect on the intestinal barrier. 16S rRNA analysis claimed that YG altered α- and β-diversity and enriched the relative abundance of class Bacilli, orders Lactobacillales and Enterobacteriales, families Lactobacillaceae and Enterobacteriaceae, genera Lactobacillus and Escherichia–Shigella, and species uncultured bacterium-Lactobacillus. Significant downregulation of cutin and suberin, wax biosynthesis, atrazine degradation, vitamin B6 metabolism, phosphotransferase system (PTS), steroid degradation, biosynthesis of unsaturated fatty acids, aminobenzoate degradation and quorum sensing and upregulation of ascorbate and aldarate metabolism, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, steroid biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, sesquiterpenoid and triterpenoid biosynthesis, lysine degradation, and ubiquinone and other terpenoid-quinone biosyntheses were observed in YG-treated hens, as substantiated by the findings of untargeted metabolomics analysis. Overall, YG manifests prebiotic properties by altering gut microbiome and metabolite profiles and can downregulate the intestinal mucosal immune response of breeder hens.
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Affiliation(s)
- Wenrui Zhen
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.,State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yujing Shao
- College of Biology, China Agricultural University, Beijing, China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yuanyuan Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fangshen Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Waseem Abbas
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhong Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. J Anim Sci Biotechnol 2021; 12:119. [PMID: 34857055 PMCID: PMC8638651 DOI: 10.1186/s40104-021-00640-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Heath Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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6
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He C, Lei J, Yao Y, Qu X, Chen J, Xie K, Wang X, Yi Q, Xiao B, Guo S, Zou X. Black Soldier Fly ( Hermetia illucens) Larvae Meal Modulates Intestinal Morphology and Microbiota in Xuefeng Black-Bone Chickens. Front Microbiol 2021; 12:706424. [PMID: 34603233 PMCID: PMC8482533 DOI: 10.3389/fmicb.2021.706424] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Abstract
The addition of Hermetia illucens larvae meal (HILM) to the feed could contribute to particular antimicrobial and intestinal health in animal husbandry. This study was conducted to investigate the effects of HILM on intestinal morphology and microbial diversity in different intestinal segments of Xuefeng black-bone chickens. All of 432 birds (45 weeks old) were randomly assigned to four equal groups with six replicates and 18 hens in each replicate: (A) basal diet, (B) basal diet with 1% HILM, (C) basal diet with 3% HILM, and (D) basal diet with 5% HILM. The results showed that, compared with the basal diet group, the HILM supplement significantly increased the abundance-based coverage estimator (ACE) and Chao index in cecum (p < 0.05). Diet with 1% HILM significantly increased the villus height (VH) of the duodenum (p < 0.05) and cecum microbial diversity as represented by the Simpson index (p < 0.05). In particular, 1% HILM displayed a markedly increase in the genus unclassified Bacteroidales (cecum, p < 0.05). A basal diet with 3% HILM markedly increased the beneficial genus Romboutsia (jejunum, p < 0.05). Also, principal component analysis (PCA) cluster analysis showed that 3% of HILM was more individual than other groups (p < 0.05). However, 5% HILM decreased the VH and the ratio of villus height to crypt depth (VH/CD) of the jejunum and increased beneficial bacteria such as Staphylococcus (p < 0.05), which was regarded as pathogenetic genera. In conclusion, we found that HILM improved intestinal morphology and increased microbiological diversity and species abundance. Together, dietary supplementation of 1 or 3% HILM might benefit the intestinal morphology and intestinal microbiota of Xuefeng black-bone chicken. However, the addition of 5% HILM could decrease VH and the ratio of VH/CD of the jejunum and increased pathogenetic genera. HILM was an excellent protein substitute for Xuefeng black-bone chickens, which could meet the nutritional requirements under the condition of less feed. These results provide information for HILM meal as an alternative source of soybean meal in Xuefeng black-bone chickens’ feed.
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Affiliation(s)
- Changqing He
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jiaxing Lei
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yaling Yao
- Huaihua Animal Husbandry and Fishery Affairs Center, Huaihua, China
| | - Xiangyong Qu
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jifa Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.,College of Life Science and Resources and Environment, Yichun University, Yichun, China
| | - Kailai Xie
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China
| | - Xingju Wang
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China
| | - Qi Yi
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China
| | - Bing Xiao
- Hunan Yunfeifeng Agricultural Co., Ltd., Huaihua, China
| | - Songchang Guo
- Hunan Engineering Research Center of Poultry Production Safety, Hunan Agricultural University, Changsha, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaoyan Zou
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
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7
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Volf J, Crhanova M, Karasova D, Faldynova M, Kubasova T, Seidlerova Z, Sebkova A, Zeman M, Juricova H, Matiasovicova J, Foltyn M, Tvrdon Z, Rychlik I. Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production. Microorganisms 2021; 9:microorganisms9071480. [PMID: 34361916 PMCID: PMC8305510 DOI: 10.3390/microorganisms9071480] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.
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Affiliation(s)
- Jiri Volf
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Magdalena Crhanova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Daniela Karasova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Marcela Faldynova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Tereza Kubasova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Zuzana Seidlerova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Alena Sebkova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Michal Zeman
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Helena Juricova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Jitka Matiasovicova
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
| | - Marian Foltyn
- Hatchery Vodnanske Kure, Komenskeho 75, 768 11 Chropyne, Czech Republic; (M.F.); (Z.T.)
| | - Zdenek Tvrdon
- Hatchery Vodnanske Kure, Komenskeho 75, 768 11 Chropyne, Czech Republic; (M.F.); (Z.T.)
| | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (J.V.); (M.C.); (D.K.); (M.F.); (T.K.); (Z.S.); (A.S.); (M.Z.); (H.J.); (J.M.)
- Correspondence: ; Tel.: +420-533331201
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8
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Sun B, Hou L, Yang Y. The Development of the Gut Microbiota and Short-Chain Fatty Acids of Layer Chickens in Different Growth Periods. Front Vet Sci 2021; 8:666535. [PMID: 34277754 PMCID: PMC8284478 DOI: 10.3389/fvets.2021.666535] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022] Open
Abstract
A long-term observation of changes of the gut microbiota and its metabolites would be beneficial to improving the production performance of chickens. Given this, 1-day-old chickens were chosen in this study, with the aim of observing the development of the gut microbiota and gut microbial function using 16S rRNA gene sequencing and metabolites short-chain fatty acids (SCFAs) from 8 to 50 weeks. The results showed that the relative abundances of Firmicutes and genus Alistipes were higher and fiber-degradation bacteria were less at 8 weeks compared with 20 and 50 weeks (P < 0.05). Consistently, gut microbial function was enriched in ATP-binding cassette transporters, the energy metabolism pathway, and amino acid metabolism pathway at 8 weeks. In contrast, the abundance of Bacteroidetes and some SCFA-producing bacteria and fiber-degradation bacteria significantly increased at 20 and 50 weeks compared with 8 weeks (P < 0.05), and the two-component system, glycoside hydrolase and carbohydrate metabolism pathway, was significantly increased with age. The concentration of SCFAs in the cecum at 20 weeks was higher than at 8 weeks (P < 0.01), because the level of fiber and the number of dominant fiber-degradation bacteria and SCFA-producing bacteria were more those at 20 weeks. Notably, although operational taxonomic units (OTUs) and the gut microbial α-diversity including Chao1 and abundance-based coverage estimator (ACE) were higher at 50 than 20 weeks (P < 0.01), the concentration of SCFAs at 50 weeks was lower than at 20 weeks (P < 0.01), suggesting that an overly high level of microbial diversity may not be beneficial to the production of SCFAs.
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Affiliation(s)
- Baosheng Sun
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jingzhong, China
| | - Linyue Hou
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jingzhong, China
| | - Yu Yang
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jingzhong, China
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9
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Joat N, Van TTH, Stanley D, Moore RJ, Chousalkar K. Temporal dynamics of gut microbiota in caged laying hens: a field observation from hatching to end of lay. Appl Microbiol Biotechnol 2021; 105:4719-4730. [PMID: 34014348 DOI: 10.1007/s00253-021-11333-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022]
Abstract
Gut health has major implications for the general health of food-producing animals such as the layer birds used in the egg industry. In order to modulate gut microbiota for the benefit of gut health, an understanding of the dynamics and details of the development of gut microbiota is critical. The present study investigated the phylogenetic composition of the gut microbiota of a commercial layer flock raised in cages from hatch to the end of the production cycle. This study also aimed to understand the establishment and development of gut microbiota in layer chickens. Results showed that the faecal microbiota was dominated by phyla Firmicutes and Proteobacteria in the rearing phase, but Bacteroidetes in mid lay and late lay phase. The gut microbiota composition changed significantly during the transfer of the flock from the rearing to the production shed. The richness and diversity of gut microbiota increased after week 6 of the flocks age and stabilized in the mid and late lay phase. The overall dynamics of gut microbiota development was similar to that reported in earlier studies, but the phylogenetic composition at the phylum and family level was different. The production stage of the birds is one of the important factors in the development of gut microbiota. This study has contributed to a better understanding of baseline gut microbiota development over the complete life cycles in layer chickens and will help to develop strategies to improve the gut health. KEY POINTS: • Faecal microbiota of caged hens was dominated by phyla Firmicutes and Proteobacteria in the rearing phase. • The gut microbiota composition changed significantly during the transfer of the flock from the rearing to the production shed. • The richness and diversity of gut microbiota increased after week 6 of the flocks age and stabilized in the mid and late lay phase.
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Affiliation(s)
- Nitish Joat
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Thi Thu Hao Van
- School of Applied Sciences and Health Innovations Research Institute, RMIT University, Bundoora, Victoria, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, Australia
| | - Robert J Moore
- School of Applied Sciences and Health Innovations Research Institute, RMIT University, Bundoora, Victoria, Australia
| | - Kapil Chousalkar
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia.
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10
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Zhou J, Wu S, Qi G, Fu Y, Wang W, Zhang H, Wang J. Dietary supplemental xylooligosaccharide modulates nutrient digestibility, intestinal morphology, and gut microbiota in laying hens. ACTA ACUST UNITED AC 2021; 7:152-162. [PMID: 33997343 PMCID: PMC8110867 DOI: 10.1016/j.aninu.2020.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
This study was conducted to evaluate the prebiotic effects of dietary xylooligosaccharide (XOS) supplementation on performance, nutrient digestibility, intestinal morphology, and gut microbiota in laying hens. In a 12-wk experiment, a total of 288 Hy-Line Brown layers at 50 wk of age were randomly assigned into 3 dietary treatments supplemented with XOS at 0, 200 or 400 mg/kg. Each treatment had 8 replicates with 12 birds each. Hens fed XOS diets showed a lower feed-to-egg ratio during wk 7 to 12 and a higher egg yolk color value in wk 12 compared with those fed the control diet (P < 0.05). Dietary XOS supplementation improved the apparent total tract digestibility of gross energy and nitrogen at the end of the 12th wk (P < 0.05). In addition, a higher villus height-to-crypt depth ratio of the ileum was observed in XOS-added groups (P < 0.05). The high throughput sequencing analysis of bacterial 16S rRNA revealed that dietary XOS supplementation at 200 mg/kg altered cecal microbiota. Alpha diversity analysis illustrated a higher cecal bacterial richness in birds fed with XOS at 200 mg/kg. The composition of cecal microbiota modulated by the XOS addition was characterized by an increased abundance of Firmicutes along with a reduced abundance of Bacteroidetes. At the genus level, dietary XOS supplementation triggered decreases in Bacteroides and Campylobacter concurrent with increases in Lactobacillus and several short chain fatty acid producers including Desulfovibrio, Faecalitalea, Faecalicoccus, and 5 genera of family Lachnospiraceae. Collectively, dietary XOS addition improved the feed conversion ratio by modulating nutrient digestibility and ileal morphology in laying hens, which could be attributed to the enhancement of bacterial diversity and alteration of microbial composition.
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Affiliation(s)
- Jianmin Zhou
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shugeng Wu
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanghai Qi
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Fu
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Wang
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haijun Zhang
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Wang
- Laboratory of Quality & Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture & Rural Affairs, and National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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Yan C, Xiao J, Chen D, Turner SP, Li Z, Liu H, Liu W, Liu J, Chen S, Zhao X. Feed Restriction Induced Changes in Behavior, Corticosterone, and Microbial Programming in Slow- and Fast-Growing Chicken Breeds. Animals (Basel) 2021; 11:ani11010141. [PMID: 33440656 PMCID: PMC7827424 DOI: 10.3390/ani11010141] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Different genotypes of slow- and fast-growing chickens have phenotypic changes in appearance, behavior, and productivity in response to artificial selection. Feed restriction and gut microbiota play a vital role in controlling food intake, nutrition, and health. However, little is known about how feed restriction, as a benefit or chronic stress, influences behavior, stress response, and gut microbial programming in slow- and fast-growing chickens. This study aimed to explore slow- and fast-growing chickens who had feed restricted to 70% of ad libitum or were given ad libitum feed for 30 days to evaluate the effects on behavior, stress response, and gut microbiota. We found that feed restriction can influence behaviors in both slow- and fast-growing breeds. Feed restriction to 70% for 30 days can influence stress response and gut microbiota composition, but some changes are evident only in slow- or only in fast-growing chickens. The study provides a better understanding of how artificial selection has affected chicken biology and their response to stress challenge. Abstract This study aimed to explore the difference between two Chinese local broilers, one slow- and one fast-growing, in their response to a stress challenge. We conducted the study on slow- (Weining chicken) and fast-growing (Jinlinghua chicken) breeds, with 50 chickens from each breed either feed restricted to 70% for 30 days as a stress or given ad libitum to evaluate the effects on behavior, corticosterone, and microbial programming. Standing behavior was more frequent while exploration was less common in fast-growing breeds compared to slow-growing breeds. Food seeking and ingestion, exploration, and drinking increased, while resting decreased in the feed restricted treatments. There was no difference in corticosterone concentration between slow- and fast-growing chickens, but the level was affected by feeding treatments, and the interaction of breed and feed restriction. At the genus-level, the relative abundance of Bacteroides and Lactobacillus was higher, while Cloacibacillus and Megasphaera was lower in the slow-growing breed compared to the fast-growing breed. Feed restricted birds had a higher abundance of Mucispirillum, but lower abundance of Cloacibacillus, Clostridium XlVa and Clostridium IV. In conclusion, feed restriction to 70% for 30 days as a chronic stress stimulation caused more activity, elevated the stress response, and altered gut microbiota composition, but some changes were only evident in slow- or fast-growing chickens.
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Affiliation(s)
- Chao Yan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
- Guizhou Nayong Professor Workstation, China Agricultural University, Bijie 553300, China;
| | - Jinlong Xiao
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
- Guizhou Nayong Professor Workstation, China Agricultural University, Bijie 553300, China;
| | - Di Chen
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
| | - Simon P. Turner
- Animal and Veterinary Sciences Department, Scotland’s Rural College, Edinburgh EH25 9RG, UK;
| | - Zhiwei Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
| | - Hao Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
| | - Wen Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
| | - Jian Liu
- Guizhou Nayong Professor Workstation, China Agricultural University, Bijie 553300, China;
| | - Siyu Chen
- Guizhou Nayong Professor Workstation, China Agricultural University, Bijie 553300, China;
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Correspondence: (S.C.); (X.Z.); Tel.: +86-0757-85517214 (S.C.); +86-010-62733417 (X.Z.)
| | - Xingbo Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (C.Y.); (J.X.); (D.C.); (Z.L.); (H.L.); (W.L.)
- Guizhou Nayong Professor Workstation, China Agricultural University, Bijie 553300, China;
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Correspondence: (S.C.); (X.Z.); Tel.: +86-0757-85517214 (S.C.); +86-010-62733417 (X.Z.)
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12
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Psychrophilic Full Scale Tubular Digester Operating over Eight Years: Complete Performance Evaluation and Microbiological Population. ENERGIES 2020. [DOI: 10.3390/en14010151] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Most biogas plants in the world run under psychrophilic conditions and are operated by small and medium farmers. There is a gap of knowledge on the performance of these systems after several years of operation. The aim of this research is to provide a complete evaluation of a psychrophilic, low-cost, tubular digester operated for eight years. The thermal performance was monitored for 50 days, and parameters such as pH, total volatile fatty acid (tVFA), chemical oxygen demand (COD) and volatile solids (VS) were measured every week for the influent and effluent. The digester operated at a stabilized slurry temperature of around 17.7 °C, with a mean organic load rate (OLR) equal to 0.52 kg VS/m3digester *d and an estimated hydraulic retention time (HRT) of 25 days. The VS reduction in the digester was around 77.58% and the COD reduction was 67 ± 3%, with a mean value for the effluent of 3.31 ± 1.20 g COD/Lt, while the tVFA decreased by 83.6 ± 15.5% and the presence of coliforms decreased 10.5%. A BioMethane potential test (BMP) for the influent and effluent showed that the digester reached a specific methane production of 0.40 Nm3CH4/kg VS and a 0.21 Nm3CH4/m3digester d with 63.1% CH4 in the biogas. These results, together with a microbiological analysis, show stabilized anaerobic digestion and a biogas production that was higher than expected for the psychrophilic range and the short HRT; this may have been due to the presence of an anaerobic digestion microorganism consortium which was extremely well-adapted to psychrophilic conditions over the eight-year study period.
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13
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Zhong R, Zhang L, Chen L, Yang X, Zhang H. Modulation of cecal microbiota in laying hens via intake of genetically modified corn with the maroACC or mCry1Ac genes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5450-5457. [PMID: 32562272 DOI: 10.1002/jsfa.10596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/24/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The present study investigated the chronic effect on the composition and proportions of the cecal microbiota of laying hens for 12 weeks after consuming two genetically modified (GM) corns containing the maroACC gene from the Agrobacterium tumefaciens strain (CC) and the mCry1Ac gene from the Bacillus thuringiensis strain (BT) in comparison with the isogenic corn (CT). RESULTS In total, 72 hens were randomly assigned to the CT corn-based diet, CC corn-based diet and BT corn-based diet. The absolute weights of abdominal fat, breast, thigh meat and organ weight were not affected by the dietary treatment. High-throughput 16S rRNA gene sequencing revealed a few differences in the composition of cecal microbiota among the treatments. The only difference with respect to bacterial family was that the cecal abundance of Porphyromonadaceae (3.46 versus 2.11%; P = 0.073) tended to be higher for birds consuming the CC diet than those birds consuming the CT diet. Birds fed the BT diet tended to have a higher abundance of Barnesiella (0.62 versus 0.13%; P = 0.057) and a lower abundance of unclassified Ruminococcaceae (0.64 versus 1.19%; P = 0.097) than those fed the CT diet. Considering beneficial intestinal Barnesiella, this decreases and ultimately clears the colonization of vancomycin-resistant Enterococcus. The unclassified Ruminococcaceae was a low-frequency and low-abundance bacterial taxa and was not associated with intestinal pathology. CONCLUSION These results indicate a similar modulation of cecal microbiota in laying hens by long-term feeding among transgenic CC corn, BT corn and non-transgenic corn and provide data for biosafety evaluation of the transgenic corn. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lilan Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoguang Yang
- National Institute of Nutrition and Food Safety, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Rodríguez-Saavedra M, González de Llano D, Beltran G, Torija MJ, Moreno-Arribas MV. Pectinatus spp. - Unpleasant and recurrent brewing spoilage bacteria. Int J Food Microbiol 2020; 336:108900. [PMID: 33129006 DOI: 10.1016/j.ijfoodmicro.2020.108900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 09/19/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022]
Abstract
Traditionally, beer has been recognised as a beverage with high microbiological stability because of the hostile growth environment posed by beer and increasing attention being paid to brewery hygiene. However, the microbiological risk has increased in recent years because of technological advances toward reducing oxygen in beers, besides the increase in novel beer styles production, such as non-pasteurised, flash pasteurised, cold sterilised, mid-strength, and alcoholic-free beer, that are more prone to spoilage bacteria. Moreover, using innovative beer ingredients like fruits and vegetables is an added cause of microbial spoilage. To maintain quality and good brand image, beer spoilage microorganisms are a critical concern for breweries worldwide. Pectinatus and Megasphaera are Gram-negative bacteria mostly found in improper brewing environments, leading to consumer complaints and financial losses. Because of the lack of compiled scientific knowledge on Pectinatus spoilage ability, this review provides a comprehensive overview of the occurrence, survival mechanisms, and the factors affecting beer spoilage Pectinatus species in the brewing process.
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Affiliation(s)
- Magaly Rodríguez-Saavedra
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain
| | - Dolores González de Llano
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Marcel·lí Domingo, 1, 43007 Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Marcel·lí Domingo, 1, 43007 Tarragona, Spain
| | - M Victoria Moreno-Arribas
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain.
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15
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Ricke SC, Rothrock MJ. Gastrointestinal microbiomes of broilers and layer hens in alternative production systems. Poult Sci 2020; 99:660-669. [PMID: 32029152 PMCID: PMC7587794 DOI: 10.1016/j.psj.2019.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 02/08/2023] Open
Abstract
Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed.
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Affiliation(s)
- Steven C Ricke
- Center for Food Safety and Food Science Department, University of Arkansas, Fayetteville, AR 72704.
| | - Michael J Rothrock
- Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens 30605, GA
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16
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Khan S, Chousalkar KK. Short-term feeding of probiotics and synbiotics modulates caecal microbiota during Salmonella Typhimurium infection but does not reduce shedding and invasion in chickens. Appl Microbiol Biotechnol 2019; 104:319-334. [PMID: 31758235 DOI: 10.1007/s00253-019-10220-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022]
Abstract
Positive modulation of gut microbiota in laying chickens may offer a strategy for reduction of Salmonella Typhimurium shedding and production of safer poultry products. In the current study, the caecal luminal microbiota of laying chicks was studied using 16S rRNA amplicon sequencing on DNA obtained from the chicks that were offered supplementation with commercial probiotics, synbiotics and/or Salmonella Typhimurium challenge. The load of Salmonella Typhimurium in various organs was quantified. Irrespective of the probiotics and synbiotics supplementation and Salmonella Typhimurium challenge, caecal microbiota was dominated by 22 distinct bacterial genera and 14 families that clustered into Actinobacteria, Proteobacteria and Firmicutes at phylum level. Taken together, probiotics and synbiotics supplementation increased (false discovery rate; FDR < 0.05) the abundance of Ruminococcus, Trabulsiella, Bifidobacterium, Holdemania and Oscillospira, indicating their role in maintaining gut health through lowering luminal pH and digestion of complex polysaccharides. Salmonella Typhimurium challenge decreased the abundance of Trabulsiella, Oscillospira, Holdemania, Coprococcus, Bifidobacterium and Lactobacillus and increased Klebsiella and Escherichia, indicating its role in caecal dysbiosis. Although probiotics and synbiotics supplementation positively modulated the caecal microbiota, they were not effective in significantly (P > 0.05) reducing Salmonella Typhimurium load in caecal tissue and invasion into vital organs such as liver and spleen. The early colonisation of laying chick caeca by probiotics and synbiotics had the potential to positively influence luminal microbiota; however, the microbial abundance and diversity were not sufficient to significantly reduce the shedding of Salmonella Typhimurium in faeces or invasion into internal organs during this study.
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Affiliation(s)
- Samiullah Khan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Kapil K Chousalkar
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia.
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17
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Shiraishi R, Yamazaki Y, Sasaki Y, Haruna M, Nakamura M. Imperfection of Commercial Inactivated Salmonella Vaccine Against Salmonella Infantis During Induced Molting in Chickens and Proposed Evaluation Method. Avian Dis 2019; 62:340-344. [PMID: 31119916 DOI: 10.1637/11354-122315-reg.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/20/2017] [Indexed: 11/05/2022]
Abstract
In the present study, we evaluated the continuance and efficacy of inactivated vaccine against Salmonella Infantis (SI) in chickens raised on a commercial farm. Chickens (88-days-old) were inoculated with 1 or 0.5 doses of commercially available trivalent inactivated Salmonella vaccine; anti-SI antibody titer was examined continuously for 11 mo thereafter. Molting was induced 11 mo after vaccination, and SI was administered orally. SI colony-forming units (CFUs) were measured in cecal feces, cecal contents, liver, and spleen samples. Anti-SI antibodies in the 1 dose vaccination group could be detected in at least 90% of cases until the end of testing. SI discharge was significantly reduced in birds treated with either dose of vaccine. However, SI CFUs were elevated in the induced molting group, regardless of vaccination dose, particularly in the cecal feces, cecal contents, and spleen. Thus, the vaccine provided remarkable protection against SI infection under ordinary rearing methods but not during induced molting. To achieve sufficient SI protective efficacy, we recommend inoculation with 1 dose of vaccine. Moreover, the efficacy of inactivated Salmonella vaccine is recommended to be evaluated by challenging chickens with live Salmonella in addition to Salmonella antibody titration.
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Affiliation(s)
- Rikiya Shiraishi
- Research Institute for Animal Science in Biochemistry and Toxicology, Hashimotodai, Midori-ku, Sagamihara, Kanagawa 252-0132, Japan,
| | - Yuko Yamazaki
- Research Institute for Animal Science in Biochemistry and Toxicology, Hashimotodai, Midori-ku, Sagamihara, Kanagawa 252-0132, Japan
| | - Yoshimasa Sasaki
- Ministry of Agriculture, Forestry and Fisheries, Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
| | - Mika Haruna
- Ministry of Agriculture, Forestry and Fisheries, Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
| | - Masayuki Nakamura
- Research Institute for Animal Science in Biochemistry and Toxicology, Hashimotodai, Midori-ku, Sagamihara, Kanagawa 252-0132, Japan
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18
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Enhanced CO2 Conversion to Acetate through Microbial Electrosynthesis (MES) by Continuous Headspace Gas Recirculation. ENERGIES 2019. [DOI: 10.3390/en12173297] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bioelectrochemical systems (BESs) is a term that encompasses a group of novel technologies able to interconvert electrical energy and chemical energy by means of a bioelectroactive biofilm. Microbial electrosynthesis (MES) systems, which branch off from BESs, are able to convert CO2 into valuable organic chemicals and fuels. This study demonstrates that CO2 reduction in MES systems can be enhanced by enriching the inoculum and improving CO2 availability to the biofilm. The proposed system is proven to be a repetitive, efficient, and selective way of consuming CO2 for the production of acetic acid, showing cathodic efficiencies of over 55% and CO2 conversions of over 80%. Continuous recirculation of the gas headspace through the catholyte allowed for a 44% improvement in performance, achieving CO2 fixation rates of 171 mL CO2 L−1·d−1, a maximum daily acetate production rate of 261 mg HAc·L−1·d−1, and a maximum acetate titer of 1957 mg·L−1. High-throughput sequencing revealed that CO2 reduction was mainly driven by a mixed-culture biocathode, in which Sporomusa and Clostridium, both bioelectrochemical acetogenic bacteria, were identified together with other species such as Desulfovibrio, Pseudomonas, Arcobacter, Acinetobacter or Sulfurospirillum, which are usually found in cathodic biofilms. Moreover, results suggest that these communities are responsible of maintaining a stable reactor performance.
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19
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Shi Z, Rothrock MJ, Ricke SC. Applications of Microbiome Analyses in Alternative Poultry Broiler Production Systems. Front Vet Sci 2019; 6:157. [PMID: 31179291 PMCID: PMC6543280 DOI: 10.3389/fvets.2019.00157] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
While most of the focus on poultry microbiome research has been directed toward conventional poultry production, there is increasing interest in characterizing microbial populations originating from alternative or non-conventional poultry production. This is in part due to the growing general popularity in locally produced foods and more specifically the attractiveness of free-range or pasture raised poultry. Most of the focus of microbiome characterization in pasture flock birds has been on live bird production, primarily on the gastrointestinal tract. Interest in environmental impacts on production responses and management strategies have been key factors for comparative microbiome studies. This has important ramifications since these birds are not only raised under different conditions, but the grower cycle can be longer and in some cases slower growing breeds used. The impact of different feed additives is also of interest with some microbiome-based studies having examined the effect of feeding these additives to birds grown under pasture flock conditions. In the future, microbiome research approaches offer unique opportunities to develop better live bird management strategies and design optimal feed additive approaches for pasture flock poultry production systems.
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Affiliation(s)
- Zhaohao Shi
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Steven C Ricke
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
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20
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Peralta-Sánchez JM, Martín-Platero AM, Ariza-Romero JJ, Rabelo-Ruiz M, Zurita-González MJ, Baños A, Rodríguez-Ruano SM, Maqueda M, Valdivia E, Martínez-Bueno M. Egg Production in Poultry Farming Is Improved by Probiotic Bacteria. Front Microbiol 2019; 10:1042. [PMID: 31178831 PMCID: PMC6543855 DOI: 10.3389/fmicb.2019.01042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most serious threats for human health in the near future. Livestock has played an important role in the appearance of antibiotic-resistant bacteria, intestinal dysbiosis in farming animals, or the spread of AMR among pathogenic bacteria of human concern. The development of alternatives like probiotics is focused on maintaining or improving production levels while diminishing these negative effects of antibiotics. To this end, we supplied the potential probiotic Enterococcus faecalis UGRA10 in the diet of laying hens at a final concentration of 108 Colony Forming Units per gram (CFU/g) of fodder. Its effects have been analyzed by: (i) investigating the response of the ileum and caecum microbiome; and (ii) analyzing the outcome on eggs production. During the second half of the experimental period (40 to 76 days), hens fed E. faecalis UGRA10 maintained egg production, while control animals dropped egg production. Supplementation diet with E. faecalis UGRA10 significantly increased ileum and caecum bacterial diversity (higher bacterial operational taxonomic unit richness and Faith’s diversity index) of laying hens, with animals fed the same diet showing a higher similarity in microbial composition. These results point out to the beneficial effects of E. faecalis UGRA10 in egg production. Future experiments are necessary to unveil the underlying mechanisms that mediate the positive response of animals to this treatment.
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Affiliation(s)
| | | | | | | | | | - Alberto Baños
- Departamento de Microbiología y Biotecnología - DMC Research Center, Granada, Spain
| | - Sonia María Rodríguez-Ruano
- Departamento de Microbiología, Universidad de Granada, Granada, Spain.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Mercedes Maqueda
- Departamento de Microbiología, Universidad de Granada, Granada, Spain
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Universidad de Granada, Granada, Spain
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Improving Anaerobic Digestion of Sewage Sludge by Hydrogen Addition: Analysis of Microbial Populations and Process Performance. ENERGIES 2019. [DOI: 10.3390/en12071228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effect of hydrogen pulse addition on digestion performance of sewage sludge was evaluated as a means for studying the increase in efficiency of methane production. Microbial communities were also evaluated to get an insight of the changes caused by the operational modifications of the digester. An energy evaluation of this alternative was performed considering the theoretical process of coupling bioelectrochemical systems (BES) for the treatment of wastewater along with hydrogen production and the subsequent anaerobic digestion. The addition of hydrogen to sewage sludge digestion resulted in an increase of 12% in biogas production over the control (1353 mL CH4 d−1 at an injection flow rate of 1938 mL H2 d−1). The liquid phase of the sludge reactor and the H2 supplemented one did not show significant differences, thus indicating that the application of hydrogen as the co-substrate was not detrimental. High-throughput sequencing analysis showed slight changes in archaeal relative abundance after hydrogen addition, whereas eubacterial community structure and composition revealed noteworthy shifts. The mass and energy balance indicated that the amount of hydrogen obtained from a hypothetical BES can be assimilated in the sludge digester, improving biogas production, but this configuration was not capable of covering all energy needs under the proposed scenario.
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Biasato I, Ferrocino I, Biasibetti E, Grego E, Dabbou S, Sereno A, Gai F, Gasco L, Schiavone A, Cocolin L, Capucchio MT. Modulation of intestinal microbiota, morphology and mucin composition by dietary insect meal inclusion in free-range chickens. BMC Vet Res 2018; 14:383. [PMID: 30514391 PMCID: PMC6278000 DOI: 10.1186/s12917-018-1690-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/09/2018] [Indexed: 11/19/2022] Open
Abstract
Background Gut health in poultry depends on the balance between the host, intestinal microbiota, intestinal microscopic features and diet. The effects of insect meal (a promising alternative protein source for poultry feed) on chicken gut morphology have recently been reported, but no data about intestinal microbiota and mucin composition modulation are available. The present study evaluated the effects of dietary Tenebrio molitor (TM) meal inclusion on gut health of free-range chickens by intestinal microbiota, morphology and mucin composition characterization. Results One hundred forty female medium-growing hybrids were divided into 2 dietary treatments (control feed [C] and 7.5% TM inclusion, with 5 replicate pens/treatment and 14 birds/pen) and slaughtered at 97 days of age (2 birds/pen for a total of 10 chickens/diet). The gut microbiota assessment on cecal content samples by 16S rRNA amplicon based sequencing showed higher alpha (Shannon, P < 0.05) and beta (Adonis and ANOSIM, P < 0.001) diversity in birds fed TM diet than C. In comparison with C group, TM birds displayed significant increase and decrease, respectively, of the relative abundances of Firmicutes and Bacteroidetes phyla, with higher Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05). The relative abundance of Clostridium, Oscillospira, Ruminococcus, Coprococcus and Sutterella genera was higher in TM chickens than C (FDR < 0.05). On the contrary, TM birds displayed significant decrease of the relative abundance of Bacteroides genus compared to the C group (FDR < 0.05). Gut morphology evaluation by morphometric analysis on small intestine revealed similar villus height, crypt depth and villus height to crypt depth ratio between C and TM birds. Characterization of gut mucin composition by periodic-acid Schiff, Alcian Blue pH 2.5 and high iron diamine staining on small and large intestine showed unaffected mucin staining intensity in TM chickens when compared to C group. Conclusions Dietary TM meal inclusion may positively modulate the gut microbiota of the free-range chickens without influencing the intestinal morphology and mucin composition. Since the rapid growth of chickens directly depends on morphological and functional integrity of the digestive tract, the gut health assessment by a post mortem multidisciplinary approach appears to be fundamental. Electronic supplementary material The online version of this article (10.1186/s12917-018-1690-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ilaria Biasato
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Elena Biasibetti
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Elena Grego
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Sihem Dabbou
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Alessandra Sereno
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Francesco Gai
- Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy.,Institute of Science of Food Production, National Research Council, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Achille Schiavone
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy. .,Institute of Multidisciplinary Research on Sustainability, University of Turin, Via Accademia Albertina 13, 10100, Turin, Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
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Zeng J, Lei C, Wang Y, Chen Y, Zhang X, Kang Z, Zhai X, Ye X, Wang H. Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge. Microb Pathog 2018; 122:174-179. [PMID: 29906541 DOI: 10.1016/j.micpath.2018.06.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 01/03/2023]
Abstract
The aim study was to explore the distribution of Salmonella Enteritidis (S. enteritidis) in internal organs and variation of cecum microbiota in newly hatched chicken after oral challenge during a 21-day period. The quantities of S. enteritidis DNA in different internal organs (heart, liver, spleen, stomach, pancreas, small intestine, blood and cecum contents) were determined by real-time fluorescent quantitative polymerase chain reaction (FQ-PCR). The result showed that all of the above-mentioned samples were positive at 12 h post inoculation (PI) after oral challenge. The highest copy numbers of S. enteritidis in all tissue were heart and liver, with about 2 × 102 to 6 × 106 copies of DNA target sequences/0.5 g. The copy number of S. enteritidis in the stomach was only lower than the heart and liver. The blood at 8 d PI, the pancreas at 10 d PI, the heart at 14 d PI and the stomach at 17 d PI didn't have a positive result. However, the liver, spleen, cecum contents and small intestine were all positive during the 21-day period. The cecum contents at 0 d PI, 4 d PI and 10 d PI from the control group and experiment group were collected for bacterial 16 S rRNA sequencing targeting the V3-V4 hypervariable region. The result showed that at the 0 d PI, the main cecum microbiota ingredient of the two-day old chicken was Enterobacteriaceae (Proteobacteria) and the other microbiology species were fewer. At the 10 d PI, the microbiota ingredient of cecum became abundant and stable mainly including the families Ruminococcaceae (Firmicutes), Enterobacteriaceae (Proteobacteria), Lachnospiraceae (Firmicutes) and clostridiacaea (Firmicutes) both of the two group, suggesting Salmonella infection with 2-day old chicken might not significantly change cecum microbiota community. The study indicated the major organs, which carried numerous S. enteritidis, providing a significantly guideline for salmonella detection in poultry and revealed the main microbiota ingredient of chicken cecum.
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Affiliation(s)
- Jinxin Zeng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Yulong Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Yanpeng Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Xiuzhong Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Zhuangzhuang Kang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Xiwen Zhai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Xiaolan Ye
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China.
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24
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Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Bioelectrochemistry 2018; 121:27-37. [DOI: 10.1016/j.bioelechem.2018.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 01/09/2023]
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26
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Locatelli A, Hiett KL, Caudill AC, Rothrock MJ. Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this affect sampling strategies for whole-house microbiomic studies? J APPL POULTRY RES 2017. [DOI: 10.3382/japr/pfw076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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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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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: 10] [Impact Index Per Article: 1.3] [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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29
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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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Robertson V, Haltli B, McCauley EP, Overy DP, Kerr RG. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae. Microorganisms 2016; 4:E23. [PMID: 27681917 PMCID: PMC5039583 DOI: 10.3390/microorganisms4030023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/01/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022] Open
Abstract
Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome.
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Affiliation(s)
- Veronica Robertson
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
| | - Brad Haltli
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
| | - Erin P McCauley
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
| | - David P Overy
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
- Department of Pathology and Microbiology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
| | - Russell G Kerr
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
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31
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McCauley EP, Haltli B, Correa H, Kerr RG. Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum. FEMS Microbiol Ecol 2016; 92:fiw147. [PMID: 27381833 DOI: 10.1093/femsec/fiw147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2016] [Indexed: 11/13/2022] Open
Abstract
The octocoral Erythropodium caribaeorum is an important species in the Caribbean coral reef community and a source of the cytotoxic natural product desmethyleleutherobin. We utilized 16S small subunit rRNA gene amplicon pyrosequencing to characterize the microbiome of E. caribaeorum collected from Florida, USA and San Salvador, The Bahamas at multiple time points. This coral was found to have a very high microbial richness with an average Chao1 estimated richness of 1464 ± 707 operational taxonomic units and average Shannon diversity index of 4.26 ± 1.65. The taxonomic class Gammaproteobacteria was a dominant member in all samples and the genus Endozoicomonas accounted for an average of 37.7% ± 30.0% of the total sequence reads. One Endozoicomonas sp. was found to be a stable member of all E. caribaeorum sequence libraries regardless of location or time of collection and accounted for 30.1% of all sequence reads. This is the first report characterizing the microbiome associated with the encrusting octocoral E. caribaeorum.
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Affiliation(s)
- Erin P McCauley
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Brad Haltli
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Hebelin Correa
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Russell G Kerr
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
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32
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Sotres A, Tey L, Bonmatí A, Viñas M. Microbial community dynamics in continuous microbial fuel cells fed with synthetic wastewater and pig slurry. Bioelectrochemistry 2016; 111:70-82. [PMID: 27243446 DOI: 10.1016/j.bioelechem.2016.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/14/2022]
Abstract
Two-chambered microbial fuel cells (MFCs) operating with synthetic wastewater and pig slurry were assessed. Additionally, the use of 2-bromoethanesulfonate (BES-Inh) was studied. The synthetic wastewater-fed MFC (MFCSW) showed a maximum power density (PDmax) of 2138mWm(-3), and the addition of BES-Inh (10mM) did not show any improvement in its performance (PDmax=2078mWm(-3)). When pig slurry was used as feed (MFCPS), PDmax increased up to 5623mWm(-3). The microbial community composition was affected by the type of substrate used. While, Pseudomonadaceae and Clostridiaceae were the most representative families within the acetate-based medium, Flavobacteriaceae, Chitinophagaceae, Comamonadaceae and Nitrosomonadaceae were predominant when pig slurry was used as feed. Otherwise, only the Eubacterial microbial community composition was strongly modified when adding BES-Inh, thus leading to an enrichment of the Bacteroidetes phylum. Oppositely, the Archaeal community was less affected by the addition of BES-Inh, and Methanosarcina sp., arose as the predominant family in both situations. Despite all the differences in microbial communities, 6 operational taxonomic units (OTUs) belonging to Bacteroidetes (Porphyromonadaceae and Marinilabiaceae) and Firmicutes (Clostridiales) were found to be common to both MFCs, also for different contents of COD and N-NH4(+), and therefore could be considered as the bioanode core microbiome.
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Affiliation(s)
- Ana Sotres
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, ctra. C-59, km 12,1. E-08140 Caldes de Montbui, Barcelona, Spain.
| | - Laura Tey
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, ctra. C-59, km 12,1. E-08140 Caldes de Montbui, Barcelona, Spain.
| | - August Bonmatí
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, ctra. C-59, km 12,1. E-08140 Caldes de Montbui, Barcelona, Spain.
| | - Marc Viñas
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, ctra. C-59, km 12,1. E-08140 Caldes de Montbui, Barcelona, Spain.
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İnceoğlu Ö, Llirós M, Crowe SA, García-Armisen T, Morana C, Darchambeau F, Borges AV, Descy JP, Servais P. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu. MICROBIAL ECOLOGY 2015; 70:596-611. [PMID: 25912922 DOI: 10.1007/s00248-015-0612-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.
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Affiliation(s)
- Özgul İnceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium.
| | - Marc Llirós
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sean A Crowe
- Departments of Microbiology and Immunology, and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | | | - Cedric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium
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Kim JE, Lillehoj HS, Hong YH, Kim GB, Lee SH, Lillehoj EP, Bravo DM. Dietary Capsicum and Curcuma longa oleoresins increase intestinal microbiome and necrotic enteritis in three commercial broiler breeds. Res Vet Sci 2015; 102:150-8. [PMID: 26412535 DOI: 10.1016/j.rvsc.2015.07.022] [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] [Received: 01/14/2015] [Revised: 07/19/2015] [Accepted: 07/28/2015] [Indexed: 01/07/2023]
Abstract
Three commercial broiler breeds were fed from hatch with a diet supplemented with Capsicum and Curcuma longa oleoresins, and co-infected with Eimeria maxima and Clostridium perfringens to induce necrotic enteritis (NE). Pyrotag deep sequencing of bacterial 16S rRNA showed that gut microbiota compositions were quite distinct depending on the broiler breed type. In the absence of oleoresin diet, the number of operational taxonomic units (OTUs), was decreased in infected Cobb, and increased in Ross and Hubbard, compared with the uninfected. In the absence of oleoresin diet, all chicken breeds had a decreased Candidatus Arthromitus, while the proportion of Lactobacillus was increased in Cobb, but decreased in Hubbard and Ross. Oleoresin supplementation of infected chickens increased OTUs in Cobb and Ross, but decreased OTUs in Hubbard, compared with unsupplemented/infected controls. Oleoresin supplementation of infected Cobb and Hubbard was associated with an increased percentage of gut Lactobacillus and decreased Selenihalanaerobacter, while Ross had a decreased fraction of Lactobacillus and increased Selenihalanaerobacter, Clostridium, Calothrix, and Geitlerinema. These results suggest that dietary Capsicum/Curcuma oleoresins reduced the negative consequences of NE on body weight and intestinal lesion, in part, through alteration of the gut microbiome in 3 commercial broiler breeds.
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Affiliation(s)
- Ji Eun Kim
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, USDA, ARS, Beltsville, MD 20705, USA.
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, USDA, ARS, Beltsville, MD 20705, USA.
| | - Yeong Ho Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, South Korea.
| | - Geun Bae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, South Korea.
| | - Sung Hyen Lee
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, USDA, ARS, Beltsville, MD 20705, USA; National Academy of Agricultural Science, Rural Development Administration, Wanju, Jeollabuk-do 565-851, South Korea.
| | - Erik P Lillehoj
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Abstract
Prebiotics are non-digestible feed ingredients that are metabolized by specific members of intestinal microbiota and provide health benefits for the host. Fermentable oligosaccharides are best known prebiotics that have received increasing attention in poultry production. They act through diverse mechanisms, such as providing nutrients, preventing pathogen adhesion to host cells, interacting with host immune systems and affecting gut morphological structure, all presumably through modulation of intestinal microbiota. Currently, fructooligosaccharides, inulin and mannanoligosaccharides have shown promising results while other prebiotic candidates such as xylooligosaccharides are still at an early development stage. Despite a growing body of evidence reporting health benefits of prebiotics in chickens, very limited studies have been conducted to directly link health improvements to prebiotic-dependent changes in the gut microbiota. This article visits the current knowledge of the chicken gastrointestinal microbiota and reviews most recent publications related to the roles played by prebiotics in modulation of the gut microbiota and immune functions. Progress in this field will help us better understand how the gut microbiota contributes to poultry health and productivity, and support the development of new prebiotic products as an alternative to in-feed antibiotics.
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Affiliation(s)
- Mohsen Pourabedin
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada
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Kettleson EM, Adhikari A, Vesper S, Coombs K, Indugula R, Reponen T. Key determinants of the fungal and bacterial microbiomes in homes. ENVIRONMENTAL RESEARCH 2015; 138:130-5. [PMID: 25707017 PMCID: PMC4385485 DOI: 10.1016/j.envres.2015.02.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The microbiome of the home is of great interest because of its possible impact on health. Our goal was to identify some of the factors that determine the richness, evenness and diversity of the home's fungal and bacterial microbiomes. METHOD Vacuumed settled dust from homes (n=35) in Cincinnati, OH, were analyzed by pyrosequencing to determine the fungal and bacterial relative sequence occurrence. The correlation coefficients between home environmental characteristics, including age of home, Environmental Relative Moldiness Index (ERMI) values, occupant number, relative humidity and temperature, as well as pets (dog and cat) were evaluated for their influence on fungal and bacterial communities. In addition, linear discriminant analysis (LDA) was used for identifying fungal and bacterial genera and species associated with those housing determinants found to be significant. RESULTS The fungal richness was found to be positively correlated with age of home (p=0.002), ERMI value (p=0.003), and relative humidity (p=0.015) in the home. However, fungal evenness and diversity were only correlated with the age of home (p=0.001). Diversity and evenness (not richness) of the bacterial microbiome in the homes were associated with dog ownership. Linear discriminant analysis showed total of 39 putative fungal genera/species with significantly higher LDA scores in high ERMI homes and 47 genera/species with significantly higher LDA scores in homes with high relative humidity. When categorized according to the age of the home, a total of 67 fungal genera/species had LDA scores above the significance threshold. Dog ownership appeared to have the most influence on the bacterial microbiome, since a total of 130 bacterial genera/species had significantly higher LDA scores in homes with dogs. CONCLUSIONS Some key determinants of the fungal and bacterial microbiome appear to be excess moisture, age of the home and dog ownership.
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Affiliation(s)
- Eric M Kettleson
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, 3223 Eden Ave., Cincinnati, OH 45267-0056, United States; ZF Steering Systems NACAM Corp, 15 Spiral Drive, Florence, KY 41042, United States.
| | - Atin Adhikari
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, 3223 Eden Ave., Cincinnati, OH 45267-0056, United States; Department of Environmental Health Sciences, Jiann-Ping Hsu College of Public Health, Georgia Southern University, 501 Forest Drive, Statesboro, GA 30460, United States.
| | - Stephen Vesper
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, 26 West M. L. King Drive, Cincinnati, OH 45268, United States.
| | - Kanistha Coombs
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, 3223 Eden Ave., Cincinnati, OH 45267-0056, United States.
| | - Reshmi Indugula
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, 3223 Eden Ave., Cincinnati, OH 45267-0056, United States.
| | - Tiina Reponen
- University of Cincinnati, Department of Environmental Health, P.O. Box 670056, 3223 Eden Ave., Cincinnati, OH 45267-0056, United States.
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Hullar MAJ, Lancaster SM, Li F, Tseng E, Beer K, Atkinson C, Wähälä K, Copeland WK, Randolph TW, Newton KM, Lampe JW. Enterolignan-producing phenotypes are associated with increased gut microbial diversity and altered composition in premenopausal women in the United States. Cancer Epidemiol Biomarkers Prev 2015; 24:546-54. [PMID: 25542830 PMCID: PMC4392386 DOI: 10.1158/1055-9965.epi-14-0262] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Lignans in plant foods are metabolized by gut bacteria to the enterolignans, enterodiol (END) and enterolactone (ENL). Enterolignans have biologic activities important to the prevention of cancer and chronic diseases. We examined the composition of the gut microbial community (GMC) as a contributor to human enterolignan exposure. METHODS We evaluated the association between the GMC in stool, urinary enterolignan excretion, and diet from a 3-day food record in 115 premenopausal (ages 40-45 years) women in the United States. Urinary enterolignans were measured using gas chromatography-mass spectroscopy. The GMC was evaluated using 454 pyrosequencing of the 16S rRNA gene. Sequences were aligned in SILVA (www.arb-silva.de). Operational taxonomic units were identified at 97% sequence similarity. Taxonomic classification was performed and alpha and beta diversity in relationship to ENL production were assessed. Multivariate analysis and regression were used to model the association between enterolignan excretion and the GMC. Bacteria associated with ENL production were identified using univariate analysis and ridge regression. RESULTS After adjusting for dietary fiber intake and adiposity, we found a significant positive association between ENL excretion and either the GMC (P = 0.0007), or the diversity of the GMC (P = 0.01). The GMC associated with high ENL production was distinct (UNIFRAC, P < 0.003, MRPP) and enriched in Moryella spp., Acetanaerobacterium spp., Fastidiosipila spp., and Streptobacillus spp. CONCLUSION Diversity and composition of the GMC are associated with increased human exposure to enterolignans. IMPACT Differences in gut microbial diversity and composition explain variation in gut metabolic processes that affect environmental exposures and influence human health. Cancer Epidemiol Biomarkers Prev; 24(3); 546-54. ©2014 AACR.
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Affiliation(s)
| | - Samuel M Lancaster
- Fred Hutchinson Cancer Research Center, Seattle, Washington. University of Washington, Seattle, Washington
| | - Fei Li
- University of Washington, Seattle, Washington
| | | | - Karlyn Beer
- University of Washington, Seattle, Washington
| | | | | | | | | | | | - Johanna W Lampe
- Fred Hutchinson Cancer Research Center, Seattle, Washington. University of Washington, Seattle, Washington
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Videnska P, Sedlar K, Lukac M, Faldynova M, Gerzova L, Cejkova D, Sisak F, Rychlik I. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life. PLoS One 2014; 9:e115142. [PMID: 25501990 PMCID: PMC4264878 DOI: 10.1371/journal.pone.0115142] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/19/2014] [Indexed: 12/21/2022] Open
Abstract
In this study we characterised the development of caecal microbiota in egg laying hens over their commercial production lifespan, from the day of hatching until 60 weeks of age. Using pyrosequencing of V3/V4 variable regions of 16S rRNA genes for microbiota characterisation, we were able to define 4 different stages of caecal microbiota development. The first stage lasted for the first week of life and was characterised by a high prevalence of Enterobacteriaceae (phylum Proteobacteria). The second stage lasted from week 2 to week 4 and was characterised by nearly an absolute dominance of Lachnospiraceae and Ruminococcaceae (both phylum Firmicutes). The third stage lasted from month 2 to month 6 and was characterised by the succession of Firmicutes at the expense of Bacteroidetes. The fourth stage was typical for adult hens in full egg production aged 7 months or more and was characterised by a constant ratio of Bacteroidetes and Firmicutes formed by equal numbers of the representatives of both phyla.
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Affiliation(s)
| | - Karel Sedlar
- The University of Technology, Brno, Czech Republic
| | - Maja Lukac
- Veterinary Research Institute, Brno, Czech Republic
| | | | | | | | | | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
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Videnska P, Rahman MM, Faldynova M, Babak V, Matulova ME, Prukner-Radovcic E, Krizek I, Smole-Mozina S, Kovac J, Szmolka A, Nagy B, Sedlar K, Cejkova D, Rychlik I. Characterization of egg laying hen and broiler fecal microbiota in poultry farms in Croatia, Czech Republic, Hungary and Slovenia. PLoS One 2014; 9:e110076. [PMID: 25329397 PMCID: PMC4199679 DOI: 10.1371/journal.pone.0110076] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/08/2014] [Indexed: 12/23/2022] Open
Abstract
Poultry meat is the most common protein source of animal origin for humans. However, intensive breeding of animals in confined spaces has led to poultry colonisation by microbiota with a zoonotic potential or encoding antibiotic resistances. In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. strA gene was present in 1 out of 10,000 bacteria. The prevalence of sul1, sul2 and tet(B) in poultry microbiota was approx. 6 times lower than that of the strA gene. tet(A) and cat were the least prevalent being present in around 3 out of 10,000,000 bacteria forming fecal microbiome. The core chicken fecal microbiota was formed by 26 different families. Rather unexpectedly, representatives of Desulfovibrionaceae and Campylobacteraceae, both capable of hydrogen utilisation in complex microbial communities, belonged among core microbiota families. Understanding the roles of individual population members in the total metabolism of the complex community may allow for interventions which might result in the replacement of Campylobacteraceae with Desulfovibrionaceae and a reduction of Campylobacter colonisation in broilers, carcasses, and consequently poultry meat products.
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Affiliation(s)
| | | | | | | | | | | | - Ivan Krizek
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Jasna Kovac
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ama Szmolka
- Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Bela Nagy
- Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | | | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
- * E-mail:
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Beulig F, Heuer VB, Akob DM, Viehweger B, Elvert M, Herrmann M, Hinrichs KU, Küsel K. Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. ISME JOURNAL 2014; 9:746-59. [PMID: 25216086 DOI: 10.1038/ismej.2014.148] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 12/13/2022]
Abstract
Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. (13)CO2 mofette soil incubations showed high label incorporations with ∼512 ng (13)C g (dry weight (dw)) soil(-1) d(-1) into the bulk soil and up to 10.7 ng (13)C g (dw) soil(-1) d(-1) into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of (13)CO2. Subdivision 1 Acidobacteriaceae assimilated (13)CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.
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Affiliation(s)
- Felix Beulig
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Verena B Heuer
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Denise M Akob
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] U.S. Geological Survey, Reston, VA, USA
| | - Bernhard Viehweger
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Martina Herrmann
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kirsten Küsel
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
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Choi JH, Kim GB, Cha CJ. Spatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens. Poult Sci 2014; 93:1942-50. [PMID: 24931967 DOI: 10.3382/ps.2014-03974] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacterial communities in the different regions of gastrointestinal tract (GIT) of broiler chickens were analyzed by pyrosequencing approach to understand microbial composition and diversity. The DNA samples extracted from 7 different regions along the GIT were subjected to bacterial-community analysis by pyrosequencing of the V1-V3 region of 16S rRNA gene. Major bacterial phyla in the chicken-gut microbiota included Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria, but Firmicutes were mostly dominant (67.3 ± 16.1% of the total sequence reads identified). Among Firmicutes, Lactobacillales, including the genera Lactobacillus and Enterococcus, were the most dominant (51.8 ± 34.5% of the total sequence reads identified) from the crop to ileum. In contrast, in the cecum and large intestine, those genera were rarely detected, and Clostridiales were dominant (55.9 ± 31.4%). Fast UniFrac analysis showed that microbial communities from the crop to jejunum of the same individual chicken were grouped together, and those from ileum, cecum, and large intestine were clustered in a more GIT-specific manner. The numbers of shared operational taxonomic units between the neighboring segments of GIT were low, ranging from 2.9 to 20.3%. However, the abundance of shared operational taxonomic units in each segment was relatively high, ranging from 61.7 to 85.0%, suggesting that substantial proportions of microbial communities were shared between each segment and its neighboring segments, comprising a core microbiota. Our results suggested that the microbial communities of 7 main segments in the chicken GIT were distinctive according to both individuals and the different segments of GIT, but their stability was maintained along the GIT.
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Affiliation(s)
- J H Choi
- Department of Systems Biotechnology, Institute of Microbiomics, and
| | - G B Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - C J Cha
- Department of Systems Biotechnology, Institute of Microbiomics, and
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42
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García-Armisen T, İnceoğlu Ö, Ouattara NK, Anzil A, Verbanck MA, Brion N, Servais P. Seasonal variations and resilience of bacterial communities in a sewage polluted urban river. PLoS One 2014; 9:e92579. [PMID: 24667680 PMCID: PMC3965440 DOI: 10.1371/journal.pone.0092579] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/23/2014] [Indexed: 12/20/2022] Open
Abstract
The Zenne River in Brussels (Belgium) and effluents of the two wastewater treatment plants (WWTPs) of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC) of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index) and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation). BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience), whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons.
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Affiliation(s)
- Tamara García-Armisen
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
| | - Özgül İnceoğlu
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
| | - Nouho Koffi Ouattara
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
| | - Adriana Anzil
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
| | - Michel A Verbanck
- Department of Water Pollution Control, Université Libre de Bruxelles, Campus Plaine, Brussels, Belgium
| | - Natacha Brion
- Analytical and Environmental Chemistry, Vrije Universiteit Brussels, Brussels, Belgium
| | - Pierre Servais
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
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Stanley D, Geier MS, Hughes RJ, Denman SE, Moore RJ. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS One 2013; 8:e84290. [PMID: 24391931 PMCID: PMC3877270 DOI: 10.1371/journal.pone.0084290] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/19/2013] [Indexed: 01/17/2023] Open
Abstract
Studies investigating the role that complex microbiotas associated with animals and humans play in health and wellbeing have been greatly facilitated by advances in DNA sequencing technology. Due to the still relatively high sequencing costs and the expense of establishing and running animal trials and collecting clinical samples, most of the studies reported in the literature are limited to a single trial and relatively small numbers of samples. Results from different laboratories, investigating similar trials and samples, have often produced quite different pictures of microbiota composition. This study investigated batch to batch variations in chicken cecal microbiota across three similar trials, represented by individually analysed samples from 207 birds. Very different microbiota profiles were found across the three flocks. The flocks also differed in the efficiency of nutrient use as indicated by feed conversion ratios. In addition, large variations in the microbiota of birds within a single trial were noted. It is postulated that the large variability in microbiota composition is due, at least in part, to the lack of colonisation of the chicks by maternally derived bacteria. The high hygiene levels maintained in modern commercial hatcheries, although effective in reducing the burden of specific diseases, may have the undesirable effect of causing highly variable bacterial colonization of the gut. Studies in humans and other animals have previously demonstrated large variations in microbiota composition when comparing individuals from different populations and from different environments but this study shows that even under carefully controlled conditions large variations in microbiota composition still occur.
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Affiliation(s)
- Dragana Stanley
- Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
- Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia
- School of Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, Australia
| | - Mark S. Geier
- Pig and Poultry Production Institute, South Australian Research and Development Institute, Roseworthy, South Australia, Australia
- Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Robert J. Hughes
- Pig and Poultry Production Institute, South Australian Research and Development Institute, Roseworthy, South Australia, Australia
- Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Stuart E. Denman
- Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, St Lucia, Queensland, Australia
| | - Robert J. Moore
- Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
- Poultry Cooperative Research Centre, University of New England, Armidale, New South Wales, Australia
- Department of Microbiology, Monash University, Clayton, Australia
- * E-mail:
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Mao S, Zhang R, Wang D, Zhu W. Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing. Anaerobe 2013; 24:12-9. [DOI: 10.1016/j.anaerobe.2013.08.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 06/17/2013] [Accepted: 08/15/2013] [Indexed: 11/16/2022]
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Correa H, Haltli B, Duque C, Kerr R. Bacterial communities of the gorgonian octocoral Pseudopterogorgia elisabethae. MICROBIAL ECOLOGY 2013; 66:972-85. [PMID: 23913197 DOI: 10.1007/s00248-013-0267-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 07/09/2013] [Indexed: 05/06/2023]
Abstract
Pseudopterogorgia elisabethae is a common inhabitant of Caribbean reefs and is a well-known source of diterpenes with diverse biological activities. Notably, this octocoral is the sole source of the pseudopterosin family of anti-inflammatory diterpenes and is harvested to supply commercial demand for these metabolites. We have characterized the composition of the bacterial community associated with P. elisabethae collected from Providencia Island, Colombia, using both culture-dependent and culture-independent approaches. Culture-independent analysis revealed that the bacterial communities were composed of eight phyla, of which Proteobacteria was the most abundant. At the class level, bacterial communities were dominated by Gammaproteobacteria (82-87 %). Additionally, operational taxonomic units related to Pseudomonas and Endozoicomonas species were the most abundant phylotypes consistently associated with P. elisabethae colonies. Culture-dependent analysis resulted in the identification of 40 distinct bacteria classified as Bacilli (15), Actinobacteria (12), Gammaproteobacteria (9), Alphaproteobacteria (3), and Betaproteobacteria (1). Only one of the 40 cultured bacteria was closely related to a dominant phylotype detected in the culture-independent study, suggesting that conventional culturing techniques failed to culture the majority of octocoral-associated bacterial diversity. To the best of our knowledge, this is the first characterization of the bacterial diversity associated with P. elisabethae.
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Affiliation(s)
- Hebelin Correa
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, District of Colombia, Colombia
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Abstract
The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana 59717-2900;
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Argañaraz-Martínez E, Babot JD, Apella MC, Perez Chaia A. Physiological and functional characteristics of Propionibacterium strains of the poultry microbiota and relevance for the development of probiotic products. Anaerobe 2013; 23:27-37. [PMID: 23973927 DOI: 10.1016/j.anaerobe.2013.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/05/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
The prevention and control of pathogens colonization through probiotics administration in poultry feeding is of increasing interest. The genus Propionibacterium is an attractive candidate for the development of probiotic cultures as they produce short chain fatty acids (SCFA) by carbohydrates fermentation. The presence of strains of this genus in hens of conventional production systems and backyard hens was investigated. Propionibacteria were isolated from the intestine and identified by physiological and biochemical tests. PCR amplification of the 16S rRNA gene of the isolates was performed and products were compared with sequences from databases. The presence of the genus Propionibacterium was demonstrated in 26% of hens and Propionibacterium acidipropionici and Propionibacterium avidum were the identified species. A comparative study of their physiological and functional characteristics was performed. P. acidipropionici strains were the most resistant to in vitro gastrointestinal digestion, but the adhesion to intestinal tissue was strain dependent. Some differences were found between both species with respect to their growth and SCFA production in an in vitro cecal water model, but all the strains were metabolically active. The production of SCFA in cecal slurries inoculated with the strain P. acidipropionici LET 105 was 30% higher than in non-inoculated samples. SCFA concentrations obtained were high enough to inhibit Salmonella enterica serovar Enteritidis when assayed in a cecal water model. P. acidipropionici LET 105 was also able to compete with Salmonella for adhesion sites on the intestinal mucosa in ex vivo assays. Results contribute to the knowledge of the species diversity of the genus Propionibacterium in the intestine of poultry and provide evidence of their potential for probiotics products development.
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Affiliation(s)
- Eloy Argañaraz-Martínez
- Centro de Referencia para Lactobacilos (CERELA)-CONICET, Chacabuco 145, T4000ILC San Miguel de Tucumán, Argentina; Universidad Nacional de Tucumán, Ayacucho 471, T4000ILC San Miguel de Tucumán, Argentina
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McCarville JL, Clarke ST, Shastri P, Liu Y, Kalmokoff M, Brooks SPJ, Green-Johnson JM. Spaceflight influences both mucosal and peripheral cytokine production in PTN-Tg and wild type mice. PLoS One 2013; 8:e68961. [PMID: 23874826 PMCID: PMC3707889 DOI: 10.1371/journal.pone.0068961] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
Spaceflight is associated with several health issues including diminished immune efficiency. Effects of long-term spaceflight on selected immune parameters of wild type (Wt) and transgenic mice over-expressing pleiotrophin under the human bone-specific osteocalcin promoter (PTN-Tg) were examined using the novel Mouse Drawer System (MDS) aboard the International Space Station (ISS) over a 91 day period. Effects of this long duration flight on PTN-Tg and Wt mice were determined in comparison to ground controls and vivarium-housed PTN-Tg and Wt mice. Levels of interleukin-2 (IL-2) and transforming growth factor-beta1 (TGF-β1) were measured in mucosal and systemic tissues of Wt and PTN-Tg mice. Colonic contents were also analyzed to assess potential effects on the gut microbiota, although no firm conclusions could be made due to constraints imposed by the MDS payload and the time of sampling. Spaceflight-associated differences were observed in colonic tissue and systemic lymph node levels of IL-2 and TGF-β1 relative to ground controls. Total colonic TGF-β1 levels were lower in Wt and PTN-Tg flight mice in comparison to ground controls. The Wt flight mouse had lower levels of IL-2 and TGF-β1 compared to the Wt ground control in both the inguinal and brachial lymph nodes, however this pattern was not consistently observed in PTN-Tg mice. Vivarium-housed Wt controls had higher levels of active TGF-β1 and IL-2 in inguinal lymph nodes relative to PTN-Tg mice. The results of this study suggest compartmentalized effects of spaceflight and on immune parameters in mice.
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Affiliation(s)
- Justin L. McCarville
- Applied Bioscience Graduate Program and Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Sandra T. Clarke
- Applied Bioscience Graduate Program and Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Padmaja Shastri
- Applied Bioscience Graduate Program and Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Yi Liu
- Università degil Studi di Genova, Dipartimento di Oncologia, Biologia e Genetica, Genova, Italy
- Istituo Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Martin Kalmokoff
- Atlantic Food and Horticulture Research Center, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, Canada
| | | | - Julia M. Green-Johnson
- Applied Bioscience Graduate Program and Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
- * E-mail:
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Lenchi N, İnceoğlu Ö, Kebbouche-Gana S, Gana ML, Llirós M, Servais P, García-Armisen T. Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing. PLoS One 2013; 8:e66588. [PMID: 23805243 PMCID: PMC3689743 DOI: 10.1371/journal.pone.0066588] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/08/2013] [Indexed: 02/06/2023] Open
Abstract
The microorganisms inhabiting many petroleum reservoirs are multi-extremophiles capable of surviving in environments with high temperature, pressure and salinity. Their activity influences oil quality and they are an important reservoir of enzymes of industrial interest. To study these microbial assemblages and to assess any modifications that may be caused by industrial practices, the bacterial and archaeal communities in waters from four Algerian oilfields were described and compared. Three different types of samples were analyzed: production waters from flooded wells, production waters from non-flooded wells and injection waters used for flooding (water-bearing formations). Microbial communities of production and injection waters appeared to be significantly different. From a quantitative point of view, injection waters harbored roughly ten times more microbial cells than production waters. Bacteria dominated in injection waters, while Archaea dominated in production waters. Statistical analysis based on the relative abundance and bacterial community composition (BCC) revealed significant differences between production and injection waters at both OTUs0.03 and phylum level. However, no significant difference was found between production waters from flooded and non-flooded wells, suggesting that most of the microorganisms introduced by the injection waters were unable to survive in the production waters. Furthermore, a Venn diagram generated to compare the BCC of production and injection waters of one flooded well revealed only 4% of shared bacterial OTUs. Phylogenetic analysis of bacterial sequences indicated that Alpha-, Beta- and Gammaproteobacteria were the main classes in most of the water samples. Archaeal sequences were only obtained from production wells and each well had a unique archaeal community composition, mainly belonging to Methanobacteria, Methanomicrobia, Thermoprotei and Halobacteria classes. Many of the bacterial genera retrieved had already been reported as degraders of complex organic molecules and pollutants. Nevertheless, a large number of unclassified bacterial and archaeal sequences were found in the analyzed samples, indicating that subsurface waters in oilfields could harbor new and still-non-described microbial species.
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Affiliation(s)
- Nesrine Lenchi
- Department of Biology, Laboratory of Conservation and Valorisation of Biological Ressources, University M’Hamed Bougara of Boumerdes, Boumerdes, Algeria
- Ecology of Aquatic Systems L, Université Libre de Bruxelles, Brussels, Belgium
| | - Özgül İnceoğlu
- Ecology of Aquatic Systems L, Université Libre de Bruxelles, Brussels, Belgium
| | - Salima Kebbouche-Gana
- Department of Biology, Laboratory of Conservation and Valorisation of Biological Ressources, University M’Hamed Bougara of Boumerdes, Boumerdes, Algeria
| | - Mohamed Lamine Gana
- Center of Research and Development, Biocorrosion Laboratory (Sonatrach), Boumerdes, Algeria
| | - Marc Llirós
- Department of Genetics and microbiology, Biosciences Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Pierre Servais
- Ecology of Aquatic Systems L, Université Libre de Bruxelles, Brussels, Belgium
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50
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Bennett DC, Tun HM, Kim JE, Leung FC, Cheng KM. Characterization of cecal microbiota of the emu (Dromaius novaehollandiae). Vet Microbiol 2013; 166:304-10. [PMID: 23850439 DOI: 10.1016/j.vetmic.2013.05.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/20/2013] [Accepted: 05/22/2013] [Indexed: 01/24/2023]
Abstract
Emus (Dromaius novaehollandiae), large flightless ratites native to Australia, are farmed for their fat and meat. They are omnivorous and feed on a wide variety of plants and insects. Despite having a relatively simple gastrointestinal tract and a short digesta retention time, emus are able to digest a significant portion of the ingested dietary neutral detergent fibre. However, nothing is known about the microbial diversity in their gastrointestinal tract. In this study, we evaluated the phylogenetic diversity of the cecal microbiota of four emus (2 males, 2 females) that were fed a barley-alfalfa-canola based diet, using 454 pyrosequencing after amplification for V3-V5 region of bacterial 16S rRNA gene. Emus were slaughtered in early November, just prior to the onset of their breeding season, but after the seasonal decline in their feed intake had begun. A total of 822 operational taxonomic units (OTUs) (335.3 ± 70.5 OTUs/sample) belonging to 9 bacterial phyla were identified. The most predominant bacterial phyla were Bacteroidetes (≈ 57% of total classified diversity), Proteobacteria (≈ 24%), Fusobacteria (≈ 11.3%), and Firmicutes (≈ 7%). Our results indicate that the emus' ceca may have a higher microbial richness (Chao1: 624 ± 170 OTUs, and ACE: 586 ± 161 OTUs) than other species of birds, but they have a lower microbial diversity (Shannon diversity index: 3.4 ± 0.2, Simpson index: 0.79 ± 0.02), possibly reflecting their decrease feed intake. This is the first study to characterize the microbial community of the gastrointestinal tract of a ratite using pyrosequencing, providing a baseline for further study.
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Affiliation(s)
- Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
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