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Pohlin F, Frei C, Meyer LCR, Roch FF, Quijada NM, Conrady B, Neubauer V, Hofmeyr M, Cooper D, Stalder G, Wetzels SU. Capture and transport of white rhinoceroses ( Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis. Conserv Physiol 2023; 11:coad089. [PMID: 38026796 PMCID: PMC10673814 DOI: 10.1093/conphys/coad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.
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Affiliation(s)
- Friederike Pohlin
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
- Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
| | - Carolin Frei
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
- Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Leith C R Meyer
- Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
| | - Franz-Ferdinand Roch
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Narciso M Quijada
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Parque Científico de Villamayor, Calle Río Duero 12, 37185 Villamayor (Salamanca), Spain
| | - Beate Conrady
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark
- Complexity Science Hub Vienna, Josefstädterstr. 38, 1080 Vienna, Austria
| | - Viktoria Neubauer
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- FFoQSI - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria
| | - Markus Hofmeyr
- Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Soutpan Road, 0110 Onderstepoort, South Africa
- Great Plains Conservation and Rhinos Without Borders, Boseja, Maun, Botswana
- Rhino Recovery Fund/Wildlife Conservation Network and Oak Foundation, 1 Kingsway, London WC2B 6AN, United Kingdom
| | - Dave Cooper
- Ezemvelo KZN Wildlife, Cascades 3202, South Africa
| | - Gabrielle Stalder
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
| | - Stefanie U Wetzels
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
- FFoQSI - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria
- Tierarztpraxis Brugger, Kitzsteinhornstraße 43, 5700 Zell am See, Austria
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Zwirzitz B, Thalguter S, Wetzels SU, Stessl B, Wagner M, Selberherr E. Autochthonous fungi are central components in microbial community structure in raw fermented sausages. Microb Biotechnol 2021; 15:1392-1403. [PMID: 34739743 PMCID: PMC9049617 DOI: 10.1111/1751-7915.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Raw meat sausage represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. Starter cultures are applied to improve product stability and safety as well as flavour characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not yet been explored. We evaluate the microbiological status of four different raw meat sausages using high‐throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to the starter culture Lactobacillus sakei and the spoilage‐associated genera Acinetobacter, Pseudomonas and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Stefanie U Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
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3
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Zwirzitz B, Wetzels SU, Dixon ED, Fleischmann S, Selberherr E, Thalguter S, Quijada NM, Dzieciol M, Wagner M, Stessl B. Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events. Front Microbiol 2021; 12:632935. [PMID: 33613505 PMCID: PMC7892895 DOI: 10.3389/fmicb.2021.632935] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/13/2021] [Indexed: 12/27/2022] Open
Abstract
A large part of foodborne outbreaks related to Listeria monocytogenes are linked to meat and meat products. Especially, recontamination of meat products and deli-meat during slicing, packaging, and repackaging is in the focus of food authorities. In that regard, L. monocytogenes persistence in multi-species biofilms is one major issue, since they survive elaborate cleaning and disinfection measures. Here, we analyzed the microbial community structure throughout a meat processing facility using a combination of high-throughput full-length 16S ribosomal RNA (rRNA) gene sequencing and traditional microbiological methods. Samples were taken at different stages during meat cutting as well as from multiple sites throughout the facility environment to capture the product and the environmental associated microbiota co-occurring with Listeria spp. and L. monocytogenes. The listeria testing revealed a widely disseminated contamination (50%; 88 of 176 samples were positive for Listeria spp. and 13.6%; 24 of 176 samples were positive for L. monocytogenes). The pulsed-field gel electrophoresis (PFGE) typing evidenced 14 heterogeneous L. monocytogenes profiles with PCR-serogroup 1/2a, 3a as most dominant. PFGE type MA3-17 contributed to the resilient microbiota of the facility environment and was related to environmental persistence. The core in-house microbiota consisted mainly of the genera Acinetobacter, Pseudomonas, Psychrobacter (Proteobacteria), Anaerobacillus, Bacillus (Firmicutes), and Chryseobacterium (Bacteroidota). While the overall microbial community structure clearly differed between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria spp. in both sample groups. Specifically, our longitudinal analysis revealed association of Listeria spp. with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the built environment microbiome in the meat processing context and promoted more effective options for targeted disinfection in the analyzed facility.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Stefanie U Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Emmanuel D Dixon
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Svenja Fleischmann
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Narciso M Quijada
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Monika Dzieciol
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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4
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Brede M, Orton T, Pinior B, Roch FF, Dzieciol M, Zwirzitz B, Wagner M, Breves G, Wetzels SU. PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System. Front Microbiol 2020; 11:1813. [PMID: 32849420 PMCID: PMC7426372 DOI: 10.3389/fmicb.2020.01813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.
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Affiliation(s)
- Melanie Brede
- Institute for Physiology and Cell Biology, University of Veterinary Medicine, Hanover, Germany
| | - Theresa Orton
- Institute for Physiology and Cell Biology, University of Veterinary Medicine, Hanover, Germany
| | - Beate Pinior
- Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Franz-Ferdinand Roch
- Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Monika Dzieciol
- Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Benjamin Zwirzitz
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Martin Wagner
- Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Gerhard Breves
- Institute for Physiology and Cell Biology, University of Veterinary Medicine, Hanover, Germany
| | - Stefanie U Wetzels
- Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
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Zwirzitz B, Wetzels SU, Rabanser I, Thalguter S, Dzieciol M, Wagner M, Mann E. Culture-Independent Evaluation of Bacterial Contamination Patterns on Pig Carcasses at a Commercial Slaughter Facility. J Food Prot 2019; 82:1677-1682. [PMID: 31532249 DOI: 10.4315/0362-028x.jfp-19-103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Traditionally, the microbiological status of meat is determined by culture-based techniques, although many bacteria are not able to grow on conventional media. The aim of this study was to obtain quantitative data on total bacterial cell equivalents, as well as taxa-specific abundances, on carcass surfaces during pig slaughter using quantitative real-time PCR. We evaluated microbial contamination patterns of total bacteria, Campylobacter, Escherichia coli, Lactobacillus group, Listeria monocytogenes, Salmonella, and Pseudomonas species throughout slaughtering and on different carcass areas. In addition, we compared contamination levels of breeding sow carcasses with fattening pig carcasses, and we assessed the efficacy of carcass polishing machines under two water amount conditions. Our results demonstrate that relevant meat-spoilage organisms show similar contamination patterns to total bacteria. The highest bacterial load was detected in the stunning chute (4.08 × 105 bacterial cell equivalents per cm2) but was reduced by 3 log levels after singeing and polishing (P < 0.001). It increased again significantly by a 4.73-fold change until the classification step. Levels of Campylobacter, Lactobacillus, and Pseudomonas species and of E. coli followed a similar trend but varied between 0 and 2.49 × 104 bacterial cell equivalents per cm2. Microbial levels did not vary significantly between sampled carcass areas for any analyzed taxa. Running the polishing machine with a low water amount proved to be less prone to microbial recontamination compared with a high water amount (17.07-fold change, P = 0.024). In the studied slaughterhouse, slaughter of breeding sows did not produce microbiologically safe meat products (>104 cells per cm2) and the implementation of specific hazard analysis critical control point systems for the slaughter of breeding sows should be considered. A larger cohort from different abattoirs is needed to confirm our results and determine whether this is universally valid.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.]).,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI) GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Stefanie U Wetzels
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.]).,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI) GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Isabel Rabanser
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.])
| | - Sarah Thalguter
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.])
| | - Monika Dzieciol
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.])
| | - Martin Wagner
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.]).,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI) GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Evelyne Mann
- Institute of Milk Hygiene, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria (ORCID: https://orcid.org/0000-0002-2253-5247 [E.M.])
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Ricci S, Sandfort R, Pinior B, Mann E, Wetzels SU, Stalder G. Impact of supplemental winter feeding on ruminal microbiota of roe deer Capreolus capreolus. Wildlife Biology 2019. [DOI: 10.2981/wlb.00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Sara Ricci
- S. Ricci and G. Stalder ✉ , Res. Inst. of Wildlife Ecology, Dept of Interdisciplinary Life Sciences, Univ. of Veterinary Medicine, Austria, Savoyenstraße 1, AU-1160 Vienna, Austria. SR also at: Univ. of Camerino, Ca
| | - Robin Sandfort
- R. Sandfort, Inst. of Wildlife Biology and Game Management, Univ. of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Beate Pinior
- B. Pinior, Inst. for Veterinary Public Health, Dept for Farm Animals and Veterinary Public Health, Univ. of Veterinary Medicine, Vienna, Austria
| | - Evelyne Mann
- E. Mann and S. U. Wetzels, Inst. of Milk Hygiene, Milk Technology and Food Science, Dept for Farm Animal and Public Health in Veterinary Medicine, Univ. of Veterinary Medicine, Vienna, Austria
| | - Stefanie U. Wetzels
- E. Mann and S. U. Wetzels, Inst. of Milk Hygiene, Milk Technology and Food Science, Dept for Farm Animal and Public Health in Veterinary Medicine, Univ. of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- S. Ricci and G. Stalder ✉ , Res. Inst. of Wildlife Ecology, Dept of Interdisciplinary Life Sciences, Univ. of Veterinary Medicine, Austria, Savoyenstraße 1, AU-1160 Vienna, Austria. SR also at: Univ. of Camerino, Ca
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Petri RM, Wetzels SU, Qumar M, Khiaosa-Ard R, Zebeli Q. Adaptive responses in short-chain fatty acid absorption, gene expression, and bacterial community of the bovine rumen epithelium recovered from a continuous or transient high-grain feeding. J Dairy Sci 2019; 102:5361-5378. [PMID: 31005320 DOI: 10.3168/jds.2018-15691] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
The feeding of high-grain diets to dairy cows commonly results in lowered pH and ruminal dysbiosis, characterized by changes in absorption dynamics of short-chain fatty acids (SCFA) across the reticuloruminal wall, epithelial function, and the epithelial bacteria community structure. Therefore, the present study evaluated the effect of high-grain feeding persistence on the absorption kinetics of reticuloruminal SCFA, gene expression in the rumen epithelium, and the associated shifts in the epithelial bacteria in cows recovering from either a long-term continuous high-grain feeding model or a long-term transient high-grain feeding model. In a crossover study design, 8 nonlactating Holstein cows were fed 60% concentrate either continuously for 4 wk (continuous) or with a 1-wk break in the second week of the high-grain feeding (transient). After the high-grain feeding, all animals were fed a diet of 100% forage (recovery) for an additional 8 wk. Rumen papilla biopsies and SCFA absorption measurements were taken at the start of the trial (baseline), after the 4-wk high-grain feeding (49 d), after 2-wk recovery forage feeding (63 d), and after 8-wk recovery forage (105 d). Absorption of SCFA was determined in vivo using the washed and isolated reticulorumen technique. Rumen papillae biopsies were used for adherent bacterial DNA and host RNA extraction. The epithelial bacteria were determined using Illumina MiSeq (Microsynth AG, Balgach, Switzerland) sequencing of the 16S rRNA gene. No significant effects of the high-grain feeding model were seen for bacterial diversity. However, bacterial diversity increased with time spent in the recovery forage feeding period regardless of feeding model. The relative abundance of Acidobacteria phyla and Acetivibrio spp. increased when animals were fed a transient high-grain feeding model. A trend toward increased CLDN4 expression was observed in the continuous model. Furthermore, there were interactions between feeding model and sampling day for gene targets CD14, DRA, NHE2, NHE3, and MCT2. When comparing length of recovery, in the continuous model increased relative absorption of SCFA was sustained at 63 d but dropped to baseline measurements at 105 d. A similar pattern was found with the transient model but it did not reach significance. The only gene target that was found to significantly correlate to relative absorption of SCFA was DRA (correlation coefficient ≤ -0.41). Whereas, genera Alkalibaculum, Anaerorhabdus, Coprococcus, and Dethiobacter all showed positive correlations to gene targets for pH regulation (NHE2 and NHE3) and SCFA uptake (MCT1) but negative correlations to SCFA absorption. We conclude that while the rumen absorption and epithelial bacteria were able to recover to baseline levels after 8 wk of forage feeding, the time needed for re-establishment of homeostasis in host gene expression is longer, especially when high-grain feeding is interrupted.
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Affiliation(s)
- R M Petri
- Institute of Animal Nutrition and Functional Plant Compounds, Veterinaerplatz 1, 1210 Vienna, Austria; Animal Gut Health Research Cluster, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - S U Wetzels
- Institute of Animal Nutrition and Functional Plant Compounds, Veterinaerplatz 1, 1210 Vienna, Austria; Animal Gut Health Research Cluster, Veterinaerplatz 1, 1210 Vienna, Austria; Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - M Qumar
- Institute of Animal Nutrition and Functional Plant Compounds, Veterinaerplatz 1, 1210 Vienna, Austria
| | - R Khiaosa-Ard
- Institute of Animal Nutrition and Functional Plant Compounds, Veterinaerplatz 1, 1210 Vienna, Austria; Animal Gut Health Research Cluster, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Veterinaerplatz 1, 1210 Vienna, Austria; Animal Gut Health Research Cluster, Veterinaerplatz 1, 1210 Vienna, Austria
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Zwirzitz B, Pinior B, Metzler-Zebeli B, Handler M, Gense K, Knecht C, Ladinig A, Dzieciol M, Wetzels SU, Wagner M, Schmitz-Esser S, Mann E. Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. Front Microbiol 2019; 10:599. [PMID: 31031713 PMCID: PMC6470194 DOI: 10.3389/fmicb.2019.00599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022] Open
Abstract
Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Beate Pinior
- Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Metzler-Zebeli
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria.,Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Monika Handler
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Gense
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Christian Knecht
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Monika Dzieciol
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie U Wetzels
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | | | - Evelyne Mann
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
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Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S. Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria. Front Microbiol 2018; 9:43. [PMID: 29410661 PMCID: PMC5787071 DOI: 10.3389/fmicb.2018.00043] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Microbiota of the rumen wall constitute an important niche of rumen microbial ecology and their composition has been elucidated in different ruminants during the last years. However, the knowledge about the function of rumen wall microbes is still limited. Rumen wall biopsies were taken from three fistulated dairy cows under a standard forage-based diet and after 4 weeks of high concentrate feeding inducing a subacute rumen acidosis (SARA). Extracted RNA was used for metatranscriptome sequencing using Illumina HiSeq sequencing technology. The gene expression of the rumen wall microbial community was analyzed by mapping 35 million sequences against the Kyoto Encyclopedia for Genes and Genomes (KEGG) database and determining differentially expressed genes. A total of 1,607 functional features were assigned with high expression of genes involved in central metabolism, galactose, starch and sucrose metabolism. The glycogen phosphorylase (EC:2.4.1.1) which degrades (1->4)-alpha-D-glucans was among the highest expressed genes being transcribed by 115 bacterial genera. Energy metabolism genes were also highly expressed, including the pyruvate orthophosphate dikinase (EC:2.7.9.1) involved in pyruvate metabolism, which was covered by 177 genera. Nitrogen metabolism genes, in particular glutamate dehydrogenase (EC:1.4.1.4), glutamine synthetase (EC:6.3.1.2) and glutamate synthase (EC:1.4.1.13, EC:1.4.1.14) were also found to be highly expressed and prove rumen wall microbiota to be actively involved in providing host-relevant metabolites for exchange across the rumen wall. In addition, we found all four urease subunits (EC:3.5.1.5) transcribed by members of the genera Flavobacterium, Corynebacterium, Helicobacter, Clostridium, and Bacillus, and the dissimilatory sulfate reductase (EC 1.8.99.5) dsrABC, which is responsible for the reduction of sulfite to sulfide. We also provide in situ evidence for cellulose and cellobiose degradation, a key step in fiber-rich feed digestion, as well as oxidative stress response and oxygen scavenging at the rumen wall. Archaea, mainly Methanocaldococcus and Methanobrevibacter, were found to be metabolically active with a high number of transcripts matching to methane and carbohydrate metabolism. These findings enhance our understanding of the metabolic function of the bovine rumen wall microbiota.
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Affiliation(s)
- Evelyne Mann
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stefanie U Wetzels
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stephan Schmitz-Esser
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna, Vienna, Austria.,Department of Animal Science, Iowa State University, Ames, IA, United States
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10
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Wetzels SU, Mann E, Pourazad P, Qumar M, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S, Zebeli Q. Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge. J Dairy Sci 2016; 100:1829-1844. [PMID: 28041738 DOI: 10.3168/jds.2016-11620] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/09/2016] [Indexed: 12/19/2022]
Abstract
Subacute ruminal acidosis (SARA) is a prevalent metabolic disorder in cattle, characterized by intermittent drops in ruminal pH. This study investigated the effect of a gradual adaptation and continuously induced long-term SARA challenge diet on the epimural bacterial community structure in the rumen of cows. Eight rumen-cannulated nonlactating Holstein cows were transitioned over 1 wk from a forage-based baseline feeding diet (grass silage-hay mix) to a SARA challenge diet, which they were fed for 4 wk. The SARA challenge diet consisted of 60% concentrates (dry matter basis) and 40% grass silage-hay mix. Rumen papillae biopsies were taken at the baseline, on the last day of the 1-wk adaptation, and on the last day of the 4-wk SARA challenge period; ruminal pH was measured using wireless sensors. We isolated DNA from papillae samples for 16S rRNA gene amplicon sequencing using Illumina MiSeq. Sequencing results of most abundant key phylotypes were confirmed by quantitative PCR. Although they were fed similar amounts of concentrate, cows responded differently in terms of ruminal pH during the SARA feeding challenge. Cows were therefore classified as responders (n = 4) and nonresponders (n = 4): only responders met the SARA criterion of a ruminal pH drop below 5.8 for longer than 330 min/d. Data showed that Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla, and at genus level, Campylobacter and Kingella showed highest relative abundance, at 15.5 and 7.8%, respectively. Diversity analyses revealed a significant increase of diversity after the 1-wk adaptation but a decrease of diversity and species richness after the 4-wk SARA feeding challenge, although without distinction between responders and nonresponders. At the level of the operational taxonomic unit, we detected diet-specific shifts in epimural community structure, but in the overall epimural bacterial community structure, we found no differences between responders and nonresponders. Correlation analysis revealed significant associations between grain intake and operational taxonomic unit abundance. The study revealed major shifts in the 3 dominating phyla and, most importantly, a loss of diversity in the epimural bacterial communities during a long-term SARA diet challenge, in which 60% concentrate supply for 4 wk was instrumental rather than the magnitude of the drop of ruminal pH below 5.8.
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Affiliation(s)
- S U Wetzels
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - E Mann
- Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - P Pourazad
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - M Qumar
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - B Pinior
- Institute for Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - B U Metzler-Zebeli
- Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - M Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - S Schmitz-Esser
- Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Research Cluster, Animal Gut Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
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11
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Qumar M, Khiaosa-ard R, Pourazad P, Wetzels SU, Klevenhusen F, Kandler W, Aschenbach JR, Zebeli Q. Evidence of In Vivo Absorption of Lactate and Modulation of Short Chain Fatty Acid Absorption from the Reticulorumen of Non-Lactating Cattle Fed High Concentrate Diets. PLoS One 2016; 11:e0164192. [PMID: 27716806 PMCID: PMC5055360 DOI: 10.1371/journal.pone.0164192] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/21/2016] [Indexed: 12/31/2022] Open
Abstract
Short-chain fatty acids (SCFAs) and lactate are endproducts of rumen fermentation and important energy sources for the host ruminant. Because their rapid accumulation results in ruminal acidosis, enhancement of the absorption of SCFA and lactate across reticuloruminal wall is instrumental in increasing energy supply and preventing ruminal acidosis in cattle. This study investigated whether the reticuloruminal absorption of SCFAs and lactate was altered by different strategies of high concentrate feeding. Eight rumen-cannulated, non-lactating Holstein cows were fed a forage-only diet (baseline) and then gradually adapted over 6 d to a 60% concentrate level. Thereafter, this concentrate-rich diet was fed for 4 wk either continuously (Con; n = 8) or interruptedly (Int; n = 8). Absorption of SCFAs and lactate was determined in vivo from the experimental buffer introduced into the washed reticulorumen. The buffer contained acetate, propionate, butyrate and lactate at a concentration of 60, 30, 10 and 5 mmol/L, respectively and Cr-EDTA as a marker for correcting ruminal water fluxes. The reticuloruminal absorption after 35 and 65 min of buffer incubation was measured at the baseline, after 1 wk of 60% concentrate feeding in the interrupted model (Int-1) and after 4 wk of concentrate feeding in both feeding models (Int-4 and Con-4). Data showed that the absorption rates of individual and total SCFAs during the first 35 min of incubation of Con-4 were highest (~1.7 times compared to baseline), while Int-1 and Int-4 were similar to respective baseline. Lactate was not absorbed during forage-only baseline and 1-wk concentrate feeding, but after 4-wk feeding of concentrates in both models. In conclusion, SCFAs absorption across the reticulorumen of non-lactating cattle was enhanced by the 4-wk continuous concentrate feeding, which seems to be more advantageous in terms of rumen acidosis prevention compared to the interrupted feeding model. The study provides evidence of lactate absorption across the reticulorumen of non-lactating cattle after both continuous and interrupted 4-wk concentrate feeding.
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Affiliation(s)
- Muhammad Qumar
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ratchaneewan Khiaosa-ard
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Poulad Pourazad
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stefanie U. Wetzels
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Fenja Klevenhusen
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Wolfgang Kandler
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences in Vienna, Tulln, Austria
| | - Jörg R. Aschenbach
- Institute of Veterinary Physiology, Free University of Berlin, Berlin, Germany
| | - Qendrim Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- * E-mail:
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12
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Mann E, Wetzels SU, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S. Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs. Meat Sci 2016; 117:36-40. [DOI: 10.1016/j.meatsci.2016.02.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/08/2016] [Accepted: 02/22/2016] [Indexed: 02/07/2023]
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13
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Wetzels SU, Mann E, Metzler-Zebeli BU, Pourazad P, Qumar M, Klevenhusen F, Pinior B, Wagner M, Zebeli Q, Schmitz-Esser S. Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle. Front Microbiol 2016; 7:274. [PMID: 26973642 PMCID: PMC4777738 DOI: 10.3389/fmicb.2016.00274] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 02/01/2023] Open
Abstract
The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a 1-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5 and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P < 0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P < 0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
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Affiliation(s)
- Stefanie U Wetzels
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Evelyne Mann
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Barbara U Metzler-Zebeli
- Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine ViennaVienna, Austria
| | - Poulad Pourazad
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Muhammad Qumar
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Fenja Klevenhusen
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Beate Pinior
- Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Martin Wagner
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Stephan Schmitz-Esser
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department of Animal Science, Iowa State UniversityAmes, IA, USA
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Mann E, Pinior B, Wetzels SU, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S. The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs. Front Microbiol 2015; 6:1362. [PMID: 26696976 PMCID: PMC4678201 DOI: 10.3389/fmicb.2015.01362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 11/17/2015] [Indexed: 12/14/2022] Open
Abstract
The exploration of microbiomes in lymphatic organs is relevant for basic and applied research into explaining microbial translocation processes and understanding cross-contamination during slaughter. This study aimed to investigate whether metabolically active bacteria (MAB) could be detected within tonsils and mandibular lymph nodes (MLNs) of pigs. The hypervariable V1-V2 region of the bacterial 16S rRNA genes was amplified from cDNA from tonsils and MLNs of eight clinically healthy slaughter pigs. Pyrosequencing yielded 82,857 quality-controlled sequences, clustering into 576 operational taxonomic units (OTUs), which were assigned to 230 genera and 16 phyla. The actual number of detected OTUs per sample varied highly (23–171 OTUs). Prevotella zoogleoformans and Serratia proteamaculans (best type strain hits) were most abundant (10.6 and 41.8%, respectively) in tonsils and MLNs, respectively. To explore bacterial correlation patterns between samples of each tissue, pairwise Spearman correlations (rs) were calculated. In total, 194 strong positive and negative correlations |rs| ≥ 0.6 were found. We conclude that (i) lymphatic organs harbor a high diversity of MAB, (ii) the occurrence of viable bacteria in lymph nodes is not restricted to pathological processes and (iii) lymphatic tissues may serve as a contamination source in pig slaughterhouses. This study confirms the necessity of the EFSA regulation with regard to a meat inspection based on visual examinations to foster a minimization of microbial contamination.
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Affiliation(s)
- Evelyne Mann
- Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria ; Research Cluster 'Animal Gut Health', Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Beate Pinior
- Institute for Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Stefanie U Wetzels
- Research Cluster 'Animal Gut Health', Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria ; Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Barbara U Metzler-Zebeli
- Research Cluster 'Animal Gut Health', Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria ; University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria ; Research Cluster 'Animal Gut Health', Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Stephan Schmitz-Esser
- Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria ; Research Cluster 'Animal Gut Health', Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
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Wetzels SU, Mann E, Metzler-Zebeli BU, Wagner M, Klevenhusen F, Zebeli Q, Schmitz-Esser S. Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. J Dairy Sci 2015; 98:5572-87. [PMID: 26051320 DOI: 10.3168/jds.2014-9166] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/19/2015] [Indexed: 12/26/2022]
Abstract
Ecological balance in the rumen is highly sensitive to concentrate-rich diets. Yet the effects of these feeding practices on the caprine bacterial epimural microbiome (CBEM), a microbial community with putative important physiological functions in the rumen, are largely unexplored. This study aimed to investigate the effect of dietary concentrate amount on ruminal CBEM. Seventeen growing goats were fed diets with 0 [n=5; 6.2MJ of metabolizable energy (ME)/d], 30 (n=6; 7.3MJ of /d), or 60% (n=6; 10.2MJ of ME/d) concentrate for 6 wk. Two hours after their last feeding, goats were euthanized and tissue samples of the ventral rumen wall were collected, washed in phosphate-buffered saline to detach loosely attached bacteria, and stored at -20°C for further processing. Genomic DNA was isolated from thawed rumen mucosa samples and used for Roche/454 Life Science (Branford, CT) 16S rRNA gene amplicon pyrosequencing yielding 122,458 reads. Pyrosequencing data were clustered into 1,879 operational taxonomic units (OTU; 0.03 distance level). Pyrosequencing revealed Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetes as the most abundant phyla (97.7%). Compared with the 30% group, both the 60 and 0% concentrate groups harbored significantly more Firmicutes and SR1, respectively. On an OTU level, a Bergeriella-related OTU was most abundant in the CBEM, followed by 2 Campylobacter OTU, which responded differently to diets: 1 OTU was significantly increased whereas the other significantly decreased with highest concentrate amount in the diet. At the genus level, the 0% concentrate group harbored increased Kingella-like sequences compared with the other feeding groups. Furthermore, the 0% concentrate group tended to have more Bergeriella than the 30 and 60% concentrate groups. The genus Bergeriella was significantly decreased in the 60% feeding group compared with the other diets. In conclusion, this is the first report of CBEM using deep-sequencing methods on the genus and OTU level, and our study revealed major shifts in the CBEM in response to concentrate-rich diets with potential health relevance in goats.
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Affiliation(s)
- S U Wetzels
- Institute of Animal Nutrition and Functional Plant Compounds, 1210 Vienna, Austria; Institute for Milk Hygiene, Milk Technology and Food Science, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria
| | - E Mann
- Institute for Milk Hygiene, Milk Technology and Food Science, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria
| | - B U Metzler-Zebeli
- Research Cluster Animal Gut Health, 1210 Vienna, Austria; University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - M Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria
| | - F Klevenhusen
- Institute of Animal Nutrition and Functional Plant Compounds, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria
| | - S Schmitz-Esser
- Institute for Milk Hygiene, Milk Technology and Food Science, 1210 Vienna, Austria; Research Cluster Animal Gut Health, 1210 Vienna, Austria.
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