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Elmagzoub WA, Idris SM, Elnaiem MHE, Mukhtar ME, Eltayeb E, Bakhiet SM, Okuni JB, Ojok L, El Sanousi SM, El Wahed AA, Gameel AA, Eltom KH. Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status. World J Microbiol Biotechnol 2024; 40:276. [PMID: 39037634 PMCID: PMC11263420 DOI: 10.1007/s11274-024-04080-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.
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Affiliation(s)
- Wisal A Elmagzoub
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
- Department of Biology and Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum North, Sudan
| | - Sanaa M Idris
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
- Department of Pathology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Marwa H E Elnaiem
- Department of Botany and Agricultural Biotechnology, Faculty of Agriculture, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Mohamed E Mukhtar
- Department of Agricultural Extension and Rural Development, Faculty of Agriculture, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - ElSagad Eltayeb
- Faculty of Medicine, Al Neelain University/Ibn Sina Specialised Hospital, Street 17-21, Alamarat, 12217, Khartoum, Sudan
| | - Sahar M Bakhiet
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Julius B Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Lonzy Ojok
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P. O. Box 7062, Kampala, Uganda
- Department of Pathology, Faculty of Medicine, Gulu University, P.O.Box 166, Gulu, Uganda
| | - Sulieman M El Sanousi
- Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Ahmed Abd El Wahed
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, An den Tierkliniken 1, 04103, Leipzig, Germany.
| | - Ahmed A Gameel
- Department of Pathology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Kamal H Eltom
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan.
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Ossa-Trujillo C, Taylor EA, Sarwar F, Vinasco J, Jordan ER, Buitrago JAG, Hagevoort GR, Lawhon SD, Piñeiro JM, Galloway-Peña J, Norman KN, Scott HM. Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis. Microorganisms 2023; 11:2728. [PMID: 38004740 PMCID: PMC10673576 DOI: 10.3390/microorganisms11112728] [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: 09/29/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.
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Affiliation(s)
- Claudia Ossa-Trujillo
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Ethan A. Taylor
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
| | - Fatima Sarwar
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
| | - Javier Vinasco
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
| | - Ellen R. Jordan
- Department of Animal Science, Texas A&M University, Dallas, TX 75252, USA;
| | - Jose A. García Buitrago
- Department of Extension Animal Sciences and Natural Resources, New Mexico State University, Clovis, NM 88101, USA; (J.A.G.B.); (G.R.H.)
| | - G. Robert Hagevoort
- Department of Extension Animal Sciences and Natural Resources, New Mexico State University, Clovis, NM 88101, USA; (J.A.G.B.); (G.R.H.)
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
| | - Juan M. Piñeiro
- Department of Animal Science, Texas A&M University, Amarillo, TX 79106, USA;
| | - Jessica Galloway-Peña
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
| | - Keri N. Norman
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Harvey Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences Texas A&M University, College Station, TX 77843, USA; (E.A.T.); (F.S.); (J.V.); (S.D.L.); (J.G.-P.)
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Jia X, He Y, Kang Z, Chen S, Sun W, Wang J, Lai S. Comparison of Fecal Microbiota Communities between Primiparous and Multiparous Cows during Non-Pregnancy and Pregnancy. Animals (Basel) 2023; 13:ani13050869. [PMID: 36899725 PMCID: PMC10000135 DOI: 10.3390/ani13050869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Imbalances in the gut microbiota composition may lead to several reproductive disorders and diseases during pregnancy. This study investigates the fecal microbiome composition between primiparous and multiparous cows during non-pregnancy and pregnancy to analyze the host-microbial balance at different stages. The fecal samples obtained from six cows before their first pregnancy (BG), six cows during their first pregnancy (FT), six open cows with more than three lactations (DCNP), and six pregnant cows with more than three lactations (DCP) were subjected to 16S rRNA sequencing, and a differential analysis of the fecal microbiota composition was performed. The three most abundant phyla in fecal microbiota were Firmicutes (48.68%), Bacteroidetes (34.45%), and Euryarchaeota (15.42%). There are 11 genera with more than 1.0% abundance at the genus level. Both alpha diversity and beta diversity showed significant differences among the four groups (p < 0.05). Further, primiparous women were associated with a profound alteration of the fecal microbiota. The most representative taxa included Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG_003, Christensenellaceae_R_7_group, Ruminococcaceae UCG-005, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Methanobrevibacter, and [Eubacterium] coprostanoligenes group, which were associated with energy metabolism and inflammation. The findings indicate that host-microbial interactions promote adaptation to pregnancy and will benefit the development of probiotics or fecal transplantation for treating dysbiosis and preventing disease development during pregnancy.
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Luo S, Wang Y, Kang X, Liu P, Wang G. Research progress on the association between mastitis and gastrointestinal microbes in dairy cows and the effect of probiotics. Microb Pathog 2022; 173:105809. [PMID: 36183956 DOI: 10.1016/j.micpath.2022.105809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022]
Abstract
Mastitis in dairy cows affects milk quality and thereby constrains the development of the dairy industry. A clear understanding of the pathogenesis of mastitis can help its treatment. Mastitis is caused by the invasion of pathogenic bacteria into the mammary gland through the mammary ducts. However, recent studies suggested that an endogenous entero-mammary pathway in dairy cattle might also be playing an important role in regulating mastitis. Also, probiotic intervention regulating host gut microbes has become an interesting tool to control mastitis. This review discusses the association of gastrointestinal microbes with mastitis and the mechanism of action of probiotics in dairy cows to provide new ideas for the management of mastitis in large-scale dairy farms.
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Affiliation(s)
- Shuangyan Luo
- School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Yuxia Wang
- School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Xinyun Kang
- School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Panpan Liu
- School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Guiqin Wang
- School of Agriculture, Ningxia University, 750021, Yinchuan, China.
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Williamson JR, Callaway TR, Lourenco JM, Ryman VE. Characterization of rumen, fecal, and milk microbiota in lactating dairy cows. Front Microbiol 2022; 13:984119. [PMID: 36225385 PMCID: PMC9549371 DOI: 10.3389/fmicb.2022.984119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p < 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p < 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p < 0.001). While diversity indices were not linked (p > 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.
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Sim S, Lee H, Yoon S, Seon H, Park C, Kim M. The impact of different diets and genders on fecal microbiota in Hanwoo cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:897-910. [PMID: 36287745 PMCID: PMC9574620 DOI: 10.5187/jast.2022.e71] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/05/2022]
Abstract
Bovine fecal microbiota is important for host health and its composition can be
affected by various factors, such as diet, age, species, breed, regions, and
environments. The objective of this study was to evaluate the impact of diet and
gender on fecal microbiota in Korean native Hanwoo cattle. The 16S rRNA gene
amplicon sequencing of fecal microbiota was conducted from 44 Hanwoo cattle
divided into four groups: (1) 11 heifers fed an oat hay plus total mixed ration
(TMR) diet for breeding (HOTB), (2) 11 heifers fed an early fattening TMR diet
(HEFT), (3) 11 steers fed the early fattening TMR diet (SEFT), and (4) 11 steers
fed the late fattening TMR diet (SLFT). Firmicutes and Bacteroidota were the
first and second most dominant phyla in all the samples, respectively. The
Firmicutes/Bacteroidota (F/B) ratio associated with feed efficiency was
significantly greater in the SLFT group than in the other groups. At the genus
level, Romboutsia, Paeniclostridium, and
Turicibacterwere the most abundant in the SLFT while
Akkermansia, Bacteroides, and
Monoglobus were the most abundant in the HOTB group.
Although the same early fattening TMR diet was fed to Hanwoo heifers and steers,
Marvinbryantia and Coprococcus were the
most abundant in the HEFT group while Alistipes and
Ruminococcus were the most abundant in the SEFT group.
Shannon and Simpson diversity indices were significantly lower in the SLFT group
than in the other groups. Distribution of fecal microbiota and functional
genetic profiles were significantly different among the four treatment groups.
The present study demonstrates that different diets and genders can affect fecal
microbiota and the F/B ratio may be associated with feed efficiency in Hanwoo
cattle. Our results may help develop strategies to improve gut health and
productivity through manipulation of fecal microbiota using the appropriate diet
considering Hanwoo cattle gender.
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Affiliation(s)
- Seunghyeun Sim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Huseong Lee
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea,Graduate School of Agricultural Science,
Tohoku University, Sendai 980-0845, Japan
| | - Sang Yoon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Hyeonsu Seon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Cheolju Park
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Minseok Kim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea,Corresponding author Minseok Kim,
Division of Animal Science, Chonnam National University, Gwangju 61186, Korea.
Tel: +82-62-530-2128, E-mail:
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The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle. Microorganisms 2022; 10:microorganisms10081672. [PMID: 36014088 PMCID: PMC9414853 DOI: 10.3390/microorganisms10081672] [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: 07/27/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress.
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