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Chai J, Zhuang Y, Cui K, Bi Y, Zhang N. Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids. MICROBIOME 2024; 12:14. [PMID: 38254181 PMCID: PMC10801991 DOI: 10.1186/s40168-023-01733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system. RESULTS In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation. CONCLUSIONS Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
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Affiliation(s)
- Jianmin Chai
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yimin Zhuang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Kai Cui
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanliang Bi
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| | - Naifeng Zhang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Liu X, Yang Z, Yang J, Wang D, Niu J, Bai B, Sun W, Ma S, Cheng Y, Hao L. A Comparative Study of Growth Performance, Blood Biochemistry, Rumen Fermentation, and Ruminal and Fecal Bacterial Structure between Yaks and Cattle Raised under High Concentrate Feeding Conditions. Microorganisms 2023; 11:2399. [PMID: 37894057 PMCID: PMC10609059 DOI: 10.3390/microorganisms11102399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
This study compared the growth performance, serum biochemical indicators, rumen fermentation parameters, rumen bacterial structure, and fecal bacterial structure of cattle and yaks fed for two months and given a feed containing concentrate of a roughage ratio of 7:3 on a dry matter basis. Compared with cattle, yak showed better growth performance. The serum biochemical results showed that the albumin/globulin ratio in yak serum was significantly higher than that in cattle. Aspartate aminotransferase, indirect bilirubin, creatine kinase, lactate dehydrogenase, and total cholesterol were significantly lower in yaks than in cattle. The rumen pH, acetate to propionate ratio, and acetate were lower in yaks than in cattle, whereas the lactate in yaks was higher than in cattle. There were significant differences in the structure of ruminal as well as fecal bacteria between cattle and yaks. The prediction of rumen bacterial function showed that there was a metabolic difference between cattle and yaks. In general, the metabolic pathway of cattle was mainly riched in a de novo synthesis of nucleotides, whereas that of yaks was mainly riched in the metabolic utilization of nutrients. This study provides a basis for understanding a rumen ecology under the condition of a high concentrate diet.
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Affiliation(s)
- Xiaojing Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhanming Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Jinfen Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Dongyang Wang
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jianzhang Niu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Binqiang Bai
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Wu Sun
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Shike Ma
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
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3
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Allworth MB, McQuillan M, McGrath SR, Wilson CS, Hernandez-Jover M. A survey on bloat in southern Australian beef production systems. Aust Vet J 2023; 101:121-126. [PMID: 36544238 DOI: 10.1111/avj.13226] [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: 07/15/2022] [Revised: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Frothy bloat, associated predominantly with grazing legume-based pastures, is considered the second most costly disease in beef cattle in southern Australia, costing $84.4 M annually. It frequently results in the sudden death of cattle. In response to concerns from cattle producers, an online survey was conducted in southern Australia in late 2020 to determine the impact of bloat, identify risk factors and determine the efficacy of current preventive measures. For 217 responses, over two-thirds (70%) of producers reported bloat occurring in the previous 12 months, with estimated morbidity and mortality rates of 3.7% and 5.0% respectively. Bloat was associated with clover or clover-dominant paddocks (79%) and was not associated with grass or grass-dominant pastures or low clover pastures (92%) nor grazing crops (27%). For bloat that occurred in the past 12 months, cattle were very commonly grazing on clover or clover-dominant paddocks (90%) and occasionally lucerne-dominated paddocks (7%). Two-thirds of producers reported having preventive measures in place when losses occurred. Bayesian Network analysis confirmed that grazing clover-based pastures for more than 7 days, yearling cattle and the months of July-September were the main risk factors for bloat occurrence, with pasture type (clover) being the most important. Conversely, no clear relationship between weather conditions and bloat occurrence was evident. This survey highlights the known risk of clover-based pastures for causing bloat in cattle, and that losses occur in many cases despite preventive measures being used. This suggests that current methods for preventing bloat in cattle are suboptimal.
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Affiliation(s)
- M B Allworth
- Fred Morley Centre, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - M McQuillan
- Fred Morley Centre, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - S R McGrath
- Fred Morley Centre, School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - C S Wilson
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - M Hernandez-Jover
- Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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Kibegwa FM, Bett RC, Gachuiri CK, Machuka E, Stomeo F, Mujibi FD. Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Affiliation(s)
- Felix M. Kibegwa
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Rawlynce C. Bett
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Charles K. Gachuiri
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Fuerniss LK, Davis HE, Belk AD, Metcalf JL, Engle TE, Scanga JA, Garry FB, Bryant TC, Martin JN. Liver abscess microbiota of feedlot steers finished in natural and traditional management programs. J Anim Sci 2022; 100:skac252. [PMID: 35938914 PMCID: PMC9645556 DOI: 10.1093/jas/skac252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Liver abscess etiology in feedlot steers involves the escape of bacteria from the digestive tract to form a polymicrobial abscess within or on the external surface of the liver. However, little is known about the effects of feedlot finishing systems on the microbial composition of the liver abscess purulent material. Liver abscesses were collected at the time of harvest from steers originating from a single feedlot managed in either a traditional program (which included tylosin phosphate supplementation) or a natural program (without tylosin phosphate supplementation). The purulent material of liver abscesses from traditionally managed steers (N = 53 abscesses) and that of naturally managed steers (N = 62 abscesses) was characterized using the V4 region of the 16S rRNA gene. Two phyla and three genera were found in greater than 1% relative abundance across all abscesses. The genus Fusobacterium was identified in all liver abscess samples and accounted for 64% of sequencing reads. Bacteroides and Porphyromonas genera accounted for 33% and 1% of reads, respectively. Trueperella was more likely to be found in the liver abscesses of naturally managed steers than traditionally managed steers (P = 0.022). Over 99% of the genus-level bacterial sequences observed across all liver abscesses belonged to Gram-negative genera. Bacteria known to colonize both the rumen and hindgut were identified within liver abscesses. No differences in alpha diversity or beta diversity were detected between liver abscess communities (between the two management programs or individual pens) when tested as richness, Shannon Diversity Index, or weighted UniFrac distances (P > 0.05). These results were consistent with previous identification of Fusobacterium necrophorum as the primary bacteriologic agent within liver abscesses and emphasized the relationship between the gastrointestinal microbiota and liver abscess formation. Though the microbiota of the liver abscess purulent material was similar between steers fed an antibiotic-free diet and those fed an antibiotic-containing diet from the same feedlot, divergence was detected in liver abscess communities with some being dominated by Fusobacterium and others being dominated by Bacteroides.
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Affiliation(s)
- Luke K Fuerniss
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Haley E Davis
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Terry E Engle
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - John A Scanga
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Franklyn B Garry
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, LLC, Johnstown, Colorado, USA
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Fuerniss LK, Kreikemeier KK, Reed LD, Cravey MD, Johnson BJ. Cecal microbiota of feedlot cattle fed a four-species Bacillus supplement. J Anim Sci 2022; 100:skac258. [PMID: 35953238 PMCID: PMC9576023 DOI: 10.1093/jas/skac258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
As commercial fed cattle consume large amounts of concentrate feedstuffs, hindgut health can be challenged. The objective of this study was to evaluate the effects of a commercially available Bacillus feed additive on cattle health outcomes and cecal microbiota of fed cattle at the time of harvest. Commercial cattle from a single feedlot were identified for characterization of cecal microbial communities using 16S ribosomal ribonucleic acid gene sequencing. All cattle were fed a common corn-based finishing diet. Control cattle (CON) were administered no treatment while treated cattle (TRT) were supplemented daily with 0.050 g of MicroSaf 4C 40 (2 billion colony forming units of Bacillus spp.; Phileo by Lesaffre, Milwaukee, WI). Immediately after harvest and evisceration, the cecal contents of cattle were sampled. After DNA extraction, amplification, and sequencing, reads from CON samples (N = 12) and TRT samples (N = 12) were assigned taxonomy using the SILVA 138 database. Total morbidity, first treatment of atypical interstitial pneumonia, and early shipments for harvest were decreased among TRT cattle compared to CON cattle (P ≤ 0.021). On average, cecal microbiota from TRT cattle had greater alpha diversity than microbiota from CON cattle as measured by Shannon diversity, Pielou's evenness, and feature richness (P < 0.010). Additionally, TRT microbial communities were different (P = 0.001) and less variable (P < 0.001) than CON microbial communities when evaluated by unweighted UniFrac distances. By relative abundance across all samples, the most prevalent phyla were Firmicutes (55.40%, SD = 15.97) and Bacteroidetes (28.17%, SD = 17.74) followed by Proteobacteria (6.75%, SD = 10.98), Spirochaetes (4.54%, SD = 4.85), and Euryarchaeota (1.77%, SD = 3.00). Spirochaetes relative abundance in TRT communities was greater than that in CON communities and was differentially abundant between treatments by ANCOM testing (W = 11); Monoglobaceae was the only family-level taxon identified as differentially abundant (W = 59; greater mean relative abundance in TRT group by 2.12 percentage points). Half (N = 6) of the CON samples clustered away from all other samples based on principal coordinates and represented cecal dysbiosis among CON cattle. The results of this study indicated that administering a four-species blend of Bacillus positively supported the cecal microbial communities of finishing cattle. Further research is needed to explore potential mechanisms of action of Bacillus DFM products in feedlot cattle.
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Affiliation(s)
- Luke K Fuerniss
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | | | - Lynn D Reed
- Phileo by Lesaffre, Milwaukee, WI 52404, USA
| | | | - Bradley J Johnson
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
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Costa-Roura S, Villalba D, Balcells J, De la Fuente G. First Steps into Ruminal Microbiota Robustness. Animals (Basel) 2022; 12:2366. [PMID: 36139226 PMCID: PMC9495070 DOI: 10.3390/ani12182366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.
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Li Y, Ma N, Ren L, Wang M, Hu L, Shen Y, Cao Y, Li Q, Li J, Gao Y. Microbiome-Metabolome Responses in Ruminal Content and Feces of Lactating Dairy Cows With N-Carbamylglutamate Supplementation Under Heat Stress. Front Vet Sci 2022; 9:902001. [PMID: 35812889 PMCID: PMC9260145 DOI: 10.3389/fvets.2022.902001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 12/17/2022] Open
Abstract
The objective of the present study was to investigate the effects of N-carbamylglutamate (NCG) supplementation on metabolic profile and microbiota in ruminal content and feces of lactating dairy cows under heat stress (HS). Forty-eight lactating Holstein cows (154 ± 13.6 days in milk) were assigned randomly to four treatments (n = 12), to receive 0, 15, 20, or 25 g/day of commercial NCG (proportion: 97.7%) for the period of 60 days. The recorded ambient temperature–humidity index (THI) suggested that the cows were exposed to HS for almost the entire experimental period (average THI: 80.6). Samples of ruminal content and feces were collected at the end of the trial (day 60) to determine the biological effects of NCG supplementation on metabolome and microbiota using mass spectrometry-based metabolomics and 16S rRNA gene sequencing techniques, respectively. Results showed that NCG supplementation enhanced the levels of ruminal microbial protein, total volatile fatty acids (VFAs), and the molar proportion of propionate in the rumen, but lowered the ruminal pH, ammonia nitrogen (NH3-N), and the ratio of acetate to propionate. NCG at doses of 20 and 25 g/day reduced the community richness and diversity of ruminal microbiota with the decrease of Shannon and Simpson diversity. Compositions of ruminal and fecal microbiotas were altered by NCG, and the PICRUSt results revealed that metabolic pathways of the bacteria, such as amino acid metabolism, energy metabolism, and pyruvate metabolism, were enriched in NCG groups. Distinct changes in the metabolomic profile of ruminal fluid were observed between the control and NCG groups. Changes of 26 metabolites mainly involved in arginine metabolism, glutamate metabolism, and nitrogen metabolism were observed associated with NCG supplementation. These results provided new insights into the effects of NCG on metabolomic profile and microbiota in ruminal content and feces, and the optimal dose of NCG supplemented to dairy cows was 20 g/hd/day, which contributed to understanding the effects of NCG on HS in lactating dairy cows.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Veterinary Biological Technology Innovation Center of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Ning Ma
- College of Veterinary Medicine, Veterinary Biological Technology Innovation Center of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Liyuan Ren
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Meimei Wang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Linqi Hu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Yufeng Cao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding, China
| | - Qiufeng Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding, China
| | - Jianguo Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding, China
- Hebei Research Institute of Dairy Industry Technology, Shijiazhuang, China
- *Correspondence: Jianguo Li
| | - Yanxia Gao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding, China
- Hebei Research Institute of Dairy Industry Technology, Shijiazhuang, China
- Yanxia Gao
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Khairunisa BH, Susanti D, Loganathan U, Teutsch CD, Campbell BT, Fiske D, Wilkinson CA, Aylward FO, Mukhopadhyay B. Dominant remodelling of cattle rumen microbiome by Schedonorus arundinaceus (tall fescue) KY-31 carrying a fungal endophyte. Access Microbiol 2022; 4:000322. [PMID: 35355877 PMCID: PMC8941964 DOI: 10.1099/acmi.0.000322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Tall fescue KY-31 is an important primary forage for beef cattle. It carries a fungal endophyte that produces ergovaline, the main cause of tall fescue toxicosis that leads to major revenue loss for livestock producers. The MaxQ, an engineered cultivar, hosts an ergovaline nonproducing strain of the fungus and consequently is nontoxic. However, it is less attractive economically. It is not known how rumen microbiome processes these two forages towards nutrient generation and ergovaline transformation. We have analysed the rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period using the 16S rRNA-V4 element as an identifier and found that KY-31 remodelled the microbiome substantially, encompassing both cellulolytic and saccharolytic functions. The effect was not evident at the whole microbiome levels but was identified by analysing the sessile and planktonic fractions separately. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. The abundances of Fibrobacter , which degrades less degradable fibres, and certain cellulolytic Firmicutes such as Pseudobutyrivibrio and Butyrivibrio 2, dropped in the sessile fraction, and these losses were apparently compensated by increased occurrences of Eubacterium and specific Ruminococcaceae and Lachnospiraceae . A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, several KY-31 induced changes, such as the low abundance of Fibrobacter and Butyrivibrio two remained in place, and their substitutes maintained significant presence. The rumen microbiome was distinct from previously reported faecal microbiomes. In summary, KY-31 and MaxQ were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study also identified candidate ergovaline transforming bacteria. It highlighted the importance of analysing sessile and planktonic fractions separately.
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Affiliation(s)
- Bela Haifa Khairunisa
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Present address: Elanco Animal Health, Greenfield, IN, USA
| | - Usha Loganathan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christopher D Teutsch
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
- Present address: University of Kentucky Research and Education Center, Princeton, KY, USA
| | - Brian T Campbell
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
- Present address: Archer Daniels Midland Company, Decatur, IL, USA
| | - David Fiske
- Shennandoah Valley Agricultural Research and Extension Center, Virginia Tech, Raphine, VA, 24472, USA
| | - Carol A Wilkinson
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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10
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Xu Y, Lei B, Zhang Q, Lei Y, Li C, Li X, Yao R, Hu R, Liu K, Wang Y, Cui Y, Wang L, Dai J, Li L, Ni W, Zhou P, Liu ZX, Hu S. ADDAGMA: A Database for Domestic Animal Gut Microbiome Atlas. Comput Struct Biotechnol J 2022; 20:891-898. [PMID: 35222847 PMCID: PMC8858777 DOI: 10.1016/j.csbj.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
We curated all publicly available high-throughput sequencing data on gut microbiomes for four domestic animal species. We compiled data for multiple levels of microbial taxa and classified the associated animal phenotypes in detail. Exhibiting the dynamic changes of animal gut microbes under different conditions. We developed a user-friendly website for browsing, searching, and displaying dynamic changes in animal gut microbes under different conditions.
Animal gut microbiomes play important roles in the health, diseases, and production of animal hosts. The volume of animal gut metagenomic data, including both 16S amplicon and metagenomic sequencing data, has been increasing exponentially in recent years, making it increasingly difficult for researchers to query, retrieve, and reanalyze experimental data and explore new hypotheses. We designed a database called the domestic animal gut microbiome atlas (ADDAGMA) to house all publicly available, high-throughput sequencing data for the gut microbiome in domestic animals. ADDAGMA enhances the availability and accessibility of the rapidly growing body of metagenomic data. We annotated microbial and metadata from four domestic animals (cattle, horse, pig, and chicken) from 356 published papers to construct a comprehensive database that is equipped with browse and search functions, enabling users to make customized, complicated, biologically relevant queries. Users can quickly and accurately obtain experimental information on sample types, conditions, and sequencing platforms, and experimental results including microbial relative abundances, microbial taxon-associated host phenotype, and P-values for gut microbes of interest. The current version of ADDAGMA includes 290,422 quantification events (changes in abundance) for 3215 microbial taxa associated with 48 phenotypes. ADDAGMA presently covers gut microbiota sequencing data from pig, cattle, horse, and chicken, but will be expanded to include other domestic animals. ADDAGMA is freely available at (http://addagma.omicsbio.info/).
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Affiliation(s)
- Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Bingbing Lei
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yunjiao Lei
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cunyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Kaiping Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yue Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yuying Cui
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832003, China
| | - Jihong Dai
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Lei Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832003, China
- Corresponding authors.
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Corresponding authors.
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
- Corresponding authors.
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11
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Corrêa PS, Jimenez CR, Mendes LW, Rymer C, Ray P, Gerdes L, da Silva VO, De Nadai Fernandes EA, Abdalla AL, Louvandini H. Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems. Front Microbiol 2021; 12:768480. [PMID: 34956130 PMCID: PMC8692951 DOI: 10.3389/fmicb.2021.768480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Caroline Rymer
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Luciana Gerdes
- Reference Laboratory on Classification and Evaluation of Animal Products, Institute of Zootechnics, Nova Odessa, Brazil
| | - Vagner Ovani da Silva
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
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12
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Petri RM, Aditya S, Humer E, Zebeli Q. Effect of an intramammary lipopolysaccharide challenge on the hindgut microbial composition and fermentation of dairy cattle experiencing intermittent subacute ruminal acidosis. J Dairy Sci 2021; 104:5417-5431. [PMID: 33663865 DOI: 10.3168/jds.2020-19496] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022]
Abstract
Feeding grain-rich diets often results in subacute ruminal acidosis (SARA), a condition associated with ruminal dysbiosis and systemic inflammation. Yet, the effect of SARA on hindgut microbiota, and whether this condition is aggravated by exogenous immune stimuli, is less understood. Therefore, the aims of this study were to determine the effects of an intermittent high-grain SARA model on the hindgut microbial community, and to evaluate whether the effects of SARA on the fecal microbiome and fermentation were further affected by an intramammary lipopolysaccharide (LPS) challenge. A total of 18 early-lactating Simmental cows were divided into 3 groups (n = 6); 2 were fed a SARA-inducing feeding regimen (60% concentrate), 1 was fed a control (CON) diet (40% concentrate). On d 30, 1 SARA group (SARA-LPS) and the CON group (CON-LPS) were intramammarily challenged with a single dose of 50 µg of LPS from Escherichia coli O26:B6, whereas the remaining 6 SARA cows (SARA-PLA) received a placebo. Using a longitudinal randomized controlled design, with grouping according to parity and days in milk), statistical analysis was performed with baseline measurements used as a covariate in a mixed model procedure. The SARA-inducing feeding challenge resulted in decreased fecal pH and increased butyrate as a proportion of total short-chain fatty acids in the feces. On d 30, SARA-challenged cows had decreased fecal diversity as shown by the Shannon and Chao1 indices and a decrease in the relative abundance of Euryarchaeota and cellulolytic genera, and numerical increases in the relative abundance of several Firmicutes associated with starch and secondary fermentation. The LPS challenge did not affect the fecal pH and short-chain fatty acids, but increased the Chao1 richness index in an interaction with the SARA challenge, and affected the relative abundance of Verrucomicrobia (1.13%), Actinobacteria (0.19%), and Spirochaetes (0.002%), suggesting an effect on the microbial ecology of the hindgut during SARA conditions. In conclusion, the SARA-inducing feeding regimen promoted important microbial changes at d 30, including reduced diversity and evenness compared with CON, whereas the external LPS challenge led to changes in the microbial community without affecting fecal fermentation properties.
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Affiliation(s)
- R M Petri
- Agriculture and Agri-Food Canada, Research and Development Centre Sherbrooke, 2000 College Street, Sherbrooke, QC, Canada, J1M 1Z7.
| | - S Aditya
- Faculty of Veterinary Medicine, Brawijaya University, Jl. Mayjen Haryono No. 169, Malang 65145, East Java, Indonesia; Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - E Humer
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 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, Veterinärplatz 1, 1210 Vienna, Austria.
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13
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Azad E, Fehr KB, Derakhshani H, Forster R, Acharya S, Khafipour E, McGeough E, McAllister TA. Interrelationships of Fiber-Associated Anaerobic Fungi and Bacterial Communities in the Rumen of Bloated Cattle Grazing Alfalfa. Microorganisms 2020; 8:microorganisms8101543. [PMID: 33036363 PMCID: PMC7601590 DOI: 10.3390/microorganisms8101543] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
Frothy bloat is major digestive disorder of cattle grazing alfalfa pastures. Among the many factors identified to contribute to the development of frothy bloat, the disruption of rumen microbiota appears to be of central importance. Anaerobic rumen fungi (ARF) play an important role in sequential breakdown and fermentation of plant polysaccharides and promote the physical disruption of plant cell walls. In the present study, we investigated the dynamics of ARF during the development of alfalfa-induced frothy bloat and in response to bloat preventive treatments. By sequencing the internal transcribed spacer (ITS1) region of metagenomic DNA from the solid fraction of rumen contents, we were able to identify eight distinct genera of ARF, including Neocallimastix, Caecomyces, Orpinomyces, Piromyces, Cyllamyces, Anaeromyces, Buwchfawromyces, and unclassified Neocallimastigaceae. Overall, transition of steers from a baseline hay diet to alfalfa pastures was associated with drastic changes in the composition of the fungal community, but the overall composition of ARF did not differ (p > 0.05) among bloated and non-bloated steers. A correlation network analysis of the proportion of ARF and ruminal bacterial communities identified hub fungal species that were negatively correlated with several bacterial species, suggesting the presence of inter-kingdom competition among these rumen microorganisms. Interestingly, the number of negative correlations among ARF and bacteria decreased with frothy bloat, indicating a potential disruption of normal microbial profiles within a bloated rumen ecosystem. A better understanding of fungal-bacterial interactions that differ among bloated and non-bloated rumen ecosystem could advance our understanding of the etiology of frothy bloat.
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Affiliation(s)
- Elnaz Azad
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Kelsey B. Fehr
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Hooman Derakhshani
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada;
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
| | - Surya Acharya
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
- Diamond V, Cedar Rapids, IA 52404, USA
| | - Emma McGeough
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Tim A. McAllister
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
- Correspondence: ; Tel.: +1-403-315-9916
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14
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Cendron F, Niero G, Carlino G, Penasa M, Cassandro M. Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing. J Appl Genet 2020; 61:593-605. [PMID: 32851593 PMCID: PMC7652803 DOI: 10.1007/s13353-020-00575-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/29/2020] [Accepted: 08/11/2020] [Indexed: 11/28/2022]
Abstract
The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy.
| | - Giovanni Niero
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Gabriele Carlino
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
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15
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Xue Y, Hu F, Guo C, Mei S, Xie F, Zeng H, Mao S. Undernutrition shifted colonic fermentation and digest-associated bacterial communities in pregnant ewes. Appl Microbiol Biotechnol 2020; 104:5973-5984. [PMID: 32415319 DOI: 10.1007/s00253-020-10662-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/17/2020] [Accepted: 05/01/2020] [Indexed: 01/06/2023]
Abstract
The objective of this study was to evaluate the effect of undernutrition on colonic microbiota and fermentation in pregnant ewes. Sixteen ewes bearing multiple fetuses for 115 days in the control (CON) and severe feed restriction (SFR) groups were fed 100% and 30% level of ad libitum feed intake, respectively. After 15-day treatment, all ewes were sacrificed to collect colonic digesta samples to extract DNA for 16S rRNA sequencing and to detect fermentation parameters. Our data showed that SFR increased (P < 0.05) the levels of colonic propionate, isobutyrate, butyrate, isovalerate, and valerate, and slightly decreased (P < 0.1) colonic pH. The mole proportions of isobutyrate, butyrate, and isovalerate were increased (P < 0.05) upon SFR while that of acetate was decreased (P < 0.05). Hematoxylin-eosin staining sections exhibited the disorderly, irregular, and loose arrangement and part sloughing of colonic epithelial cells. Furthermore, SFR decreased (P < 0.05) the diversity of colonic microbiota and changed the microbial communities. At the genus level, SFR increased (P < 0.05) the abundance of unclassified Peptococcaceae and decreased (P < 0.05) the abundances of Ruminococcus, unclassified Ruminococcaceae, and unclassified VadinBB60. Additionally, the abundances of Ruminococcus and unclassified Ruminococcaceae were positively correlated (P < 0.05) with the acetate proportion while the abundance of unclassified Peptococcaceae was negatively correlated (P < 0.05) with the percentages of isobutyrate, butyrate, and isovalerate. In summary, SFR diminished the diversity of bacteria, affected the composition of bacterial communities, and finally changed the colonic fermentation pattern and epithelial histomorphology in pregnant ewes. KEY POINTS: • Undernutrition changed colonic bacterial diversity and composition in pregnant ewes. • Microbial alteration affected colonic fermentation pattern and parameters. • Alteration of colonic microbiota and fermentation damaged epithelium histomorphology. Graphical abstract.
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Affiliation(s)
- Yanfeng Xue
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fan Hu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changzheng Guo
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijun Mei
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Xie
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongbo Zeng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China. .,College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China.
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16
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Dynamic Variations in Fecal Bacterial Community and Fermentation Profile of Holstein Steers in Response to Three Stepwise Density Diets. Animals (Basel) 2019; 9:ani9080560. [PMID: 31443265 PMCID: PMC6719243 DOI: 10.3390/ani9080560] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The gastrointestinal microbial ecosystem of cattle impacts their health and productivity. Collection of fecal samples provides a non-invasive and practicable way to explore the relationships between fecal microbiota and host productivity or health. Fecal bacteria are influenced by diet, feeding regime, animal age, and health status. However, dynamic variations in the fecal fermentation profile and microbiota composition of finishing steers in response to variable diets are limited. In the current study, we conducted an 11-month tracking investigation to uncover the dynamic variations in fecal fermentation profile and bacterial community in steers fed three stepwise density diets. We found that fecal bacterial diversity decreased as dietary density increased and as the fattening phase continued. Our results revealed that fecal organic acids and bacterial composition were influenced by diet and fattening period. Our results also indicated that time-dependent variations of fecal fermentation profile and microbiota composition exist in the long-term fattening of steers in addition to diet stimulation. This study will be beneficial to reducing fecal contamination from the origin by optimizing diet and fattening time. Abstract The objective of this study was to track the dynamic variations in fecal bacterial composition and fermentation profile of finishing steers in response to three stepwise diets varied in energy and protein density. A total of 18 Holstein steers were divided into three groups in such a way that each group contained six animals and received one of three stepwise dietary treatments. Dietary treatments were C = standard energy and protein diet, H = high energy and protein diet, and L = low energy and protein diet. Animals were fattened for 11 months with a three-phase fattening strategy. Fecal samples were collected to evaluate the dynamics of fecal fermentation and bacterial composition in response to dietary treatments and fattening phases using 16S rRNA gene sequencing. Fecal acetate, propionate, and butyrate increased with increasing density of diet and as the fattening phase continued. The relative abundances of Firmicutes and Bacteroidetes dominated and showed 56.19% and 33.58%, respectively. Higher dietary density decreased the fecal bacterial diversity, Firmicutes to Bacteroidetes ratio, and the relative abundances of Ruminococcaceae_UCG-005, Rikenellaceae_RC9_gut_group, and Bacteroides, whereas higher dietary density increased the abundance of Prevotella_9. Our results indicated that both fecal fermentation profile and bacterial composition share a time-dependent variation in response to different dietary densities. This knowledge highlights that both diet and fattening phase impact fecal fermentation profile and bacterial composition, and may provide insight into strategies to reduce fecal contamination from the origin by optimizing diet and fattening time.
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