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Guo W, Liu S, Khan MZ, Wang J, Chen T, Alugongo GM, Li S, Cao Z. Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development. J Adv Res 2024; 59:49-64. [PMID: 37423549 PMCID: PMC11081965 DOI: 10.1016/j.jare.2023.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
BACKGROUND Bovine milk is a significant substitute for human breast milk and holds great importance in infant nutrition and health. Apart from essential nutrients, bovine milk also contains bioactive compounds, including a microbiota derived from milk itself rather than external sources of contamination. AIM OF REVIEW Recognizing the profound impact of bovine milk microorganisms on future generations, our review focuses on exploring their composition, origins, functions, and applications. KEY SCIENTIFIC CONCEPTS OF REVIEW Some of the primary microorganisms found in bovine milk are also present in human milk. These microorganisms are likely transferred to the mammary gland through two pathways: the entero-mammary pathway and the rumen-mammary pathway. We also elucidated potential mechanisms by which milk microbiota contribute to infant intestinal development. The mechanisms include the enhancing of the intestinal microecological niche, promoting the maturation of immune system, strengthening the intestinal epithelial barrier function, and interacting with milk components (e.g., oligosaccharides) via cross-feeding effect. However, given the limited understanding of bovine milk microbiota, further studies are necessary to validate hypotheses regarding their origins and to explore their functions and potential applications in early intestinal development.
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Affiliation(s)
- Wenli Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Muhammad Z Khan
- Faculty of Veterinary and Animal Sciences, Department of Animal Breeding and Genetics, The University of Agriculture, Dera Ismail Khan 29220, Pakistan
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gibson M Alugongo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Patangia DV, Grimaud G, Linehan K, Ross RP, Stanton C. Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies. Antibiotics (Basel) 2023; 12:1315. [PMID: 37627735 PMCID: PMC10451192 DOI: 10.3390/antibiotics12081315] [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: 06/27/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.
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Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (D.V.P.); (R.P.R.)
- Biosciences Building, Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
| | - Ghjuvan Grimaud
- Biosciences Building, Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
| | - Kevin Linehan
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (D.V.P.); (R.P.R.)
- Biosciences Building, Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
| | - R. Paul Ross
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (D.V.P.); (R.P.R.)
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
| | - Catherine Stanton
- Biosciences Building, Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
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Coates LC, Durham SD, Storms DH, Magnuson AD, Van Hekken DL, Plumier BM, Finley JW, Fukagawa NK, Tomasula PM, Lemay DG, Picklo MJ, Barile D, Kalscheur KF, Kable ME. Associations among Milk Microbiota, Milk Fatty Acids, Milk Glycans, and Inflammation from Lactating Holstein Cows. Microbiol Spectr 2023; 11:e0402022. [PMID: 37074179 PMCID: PMC10269560 DOI: 10.1128/spectrum.04020-22] [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: 10/04/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Milk oligosaccharides (MOs) can be prebiotic and antiadhesive, while fatty acids (MFAs) can be antimicrobial. Both have been associated with milk microbes or mammary gland inflammation in humans. Relationships between these milk components and milk microbes or inflammation have not been determined for cows and could help elucidate a novel approach for the dairy industry to promote desired milk microbial composition for improvement of milk quality and reduction of milk waste. We aimed to determine relationships among milk microbiota, MFAs, MOs, lactose, and somatic cell counts (SCC) from Holstein cows, using our previously published data. Raw milk samples were collected at three time points, ranging from early to late lactation. Data were analyzed using linear mixed-effects modeling and repeated-measures correlation. Unsaturated MFA and short-chain MFA had mostly negative relationships with potentially pathogenic genera, including Corynebacterium, Pseudomonas, and an unknown Enterobacteriaceae genus but numerous positive relationships with symbionts Bifidobacterium and Bacteroides. Conversely, many MOs were positively correlated with potentially pathogenic genera (e.g., Corynebacterium, Enterococcus, and Pseudomonas), and numerous MOs were negatively correlated with the symbiont Bifidobacterium. The neutral, nonfucosylated MO composed of eight hexoses had a positive relationship with SCC, while lactose had a negative relationship with SCC. One interpretation of these trends might be that in milk, MFAs disrupt primarily pathogenic bacterial cells, causing a relative increase in abundance of beneficial microbial taxa, while MOs respond to and act on pathogenic taxa primarily through antiadhesive methods. Further research is needed to confirm the potential mechanisms driving these correlations. IMPORTANCE Bovine milk can harbor microbes that cause mastitis, milk spoilage, and foodborne illness. Fatty acids found in milk can be antimicrobial and milk oligosaccharides can have antiadhesive, prebiotic, and immune-modulatory effects. Relationships among milk microbes, fatty acids, oligosaccharides, and inflammation have been reported for humans. To our knowledge, associations among the milk microbial composition, fatty acids, oligosaccharides, and lactose have not been reported for healthy lactating cows. Identifying these potential relationships in bovine milk will inform future efforts to characterize direct and indirect interactions of the milk components with the milk microbiota. Since many milk components are associated with herd management practices, determining if these milk components impact milk microbes may provide valuable information for dairy cow management and breeding practices aimed at minimizing harmful and spoilage-causing microbes in raw milk.
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Affiliation(s)
- Laurynne C. Coates
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Sierra D. Durham
- University of California, Davis, Food Science and Technology, Davis, California, USA
| | - David H. Storms
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Andrew D. Magnuson
- U.S. Department of Agriculture—Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota, USA
| | - Diane L. Van Hekken
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - Benjamin M. Plumier
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - John W. Finley
- U.S. Department of Agriculture—Agricultural Research Service, George Washington Carver Center, Beltsville, Maryland, USA
| | - Naomi K. Fukagawa
- U.S. Department of Agriculture—Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland, USA
| | - Peggy M. Tomasula
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - Danielle G. Lemay
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Matthew J. Picklo
- U.S. Department of Agriculture—Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota, USA
| | - Daniela Barile
- University of California, Davis, Food Science and Technology, Davis, California, USA
| | - Kenneth F. Kalscheur
- U.S. Department of Agriculture—Agricultural Research Service, U.S. Dairy Forage Research Center, Madison, Wisconsin, USA
| | - Mary E. Kable
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
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Mariadassou M, Nouvel LX, Constant F, Morgavi DP, Rault L, Barbey S, Helloin E, Rué O, Schbath S, Launay F, Sandra O, Lefebvre R, Le Loir Y, Germon P, Citti C, Even S. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. Anim Microbiome 2023; 5:32. [PMID: 37308970 DOI: 10.1186/s42523-023-00252-w] [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: 09/22/2022] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing. RESULTS Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (< 7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota. CONCLUSIONS This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.
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Affiliation(s)
| | | | - Fabienne Constant
- Ecole Nationale Vétérinaire d'Alfort, Université Paris-Saclay, UVSQ, INRAE, BREED, Maisons-Alfort, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France
| | - Lucie Rault
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Sarah Barbey
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | | | - Olivier Rué
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Frederic Launay
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | - Olivier Sandra
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Rachel Lefebvre
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Yves Le Loir
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Pierre Germon
- INRAE, Université de Tours, UMR ISP, 37380, Nouzilly, France
| | | | - Sergine Even
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France.
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Rötzer V, Wenderlein J, Wiesinger A, Versen F, Rauch E, Straubinger RK, Zeiler E. Bovine Udder Health: From Standard Diagnostic Methods to New Approaches-A Practical Investigation of Various Udder Health Parameters in Combination with 16S rRNA Sequencing. Microorganisms 2023; 11:1311. [PMID: 37317285 DOI: 10.3390/microorganisms11051311] [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: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Bovine udder health is an important factor for animal wellbeing and the dairy farm economy. Thus, researchers aim to understand factors causing mastitis. The gold standard for diagnosing mastitis in cows is the conventional culturing of milk samples. However, during the last few years, the use of molecular methods has increased. These methods, especially sequencing, provide a deeper insight into the diversity of the bacterial community. Yet, inconsistent results regarding the mammary microbiome have been published. This study aimed to evaluate the udder health of eight dairy cows at seven days postpartum with the standard methods in veterinary practice. Additionally, swabs from the teat canal and milk samples were analyzed using 16S rRNA gene amplicon sequencing. The sensitive low-biomass milk samples displayed only a few contaminations even though they were sampled in a field environment. In healthy udders, no bacterial communities were detected by the bacterial culture nor the 16S rRNA gene amplicons. The results from the standard examination of the cows, the cell count, and the bacteriological examination were comparable with the results from 16S rRNA gene amplicon sequencing when cows displayed subclinical or latent mastitis. Besides the pathogen detected in bacterial culturing, a second bacterial strain with low but significant abundance was detected by sequencing, which might aid in the understanding of mastitis incidence. In general, molecular biological approaches might lead to promising insights into pathological events in the udder and might help to understand the pathomechanism and infection source via epidemiological analyses.
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Affiliation(s)
- Verena Rötzer
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
- Chair of Animal Welfare, Ethology, Animal Hygiene and Animal Husbandry, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Jasmin Wenderlein
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Anna Wiesinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Felix Versen
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
| | - Elke Rauch
- Chair of Animal Welfare, Ethology, Animal Hygiene and Animal Husbandry, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Reinhard K Straubinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Eva Zeiler
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
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Mu Y, Qi W, Zhang T, Zhang J, Mao S. Coordinated response of milk bacterial and metabolic profiles to subacute ruminal acidosis in lactating dairy cows. J Anim Sci Biotechnol 2023; 14:60. [PMID: 37138330 PMCID: PMC10158360 DOI: 10.1186/s40104-023-00859-8] [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: 10/19/2022] [Accepted: 03/01/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Bovine milk is an important source of nutrition for human consumption, and its quality is closely associated with the microbiota and metabolites in it. But there is limited knowledge about the milk microbiome and metabolome in cows with subacute ruminal acidosis. METHODS Eight ruminally cannulated Holstein cows in mid lactation were selected for a 3-week experiment. The cows were randomly allocated into 2 groups, fed either a conventional diet (CON; 40% concentrate; dry matter basis) or a high-concentrate diet (HC; 60% concentrate; dry matter basis). RESULTS The results showed that there was a decreased milk fat percentage in the HC group compared to the CON group. The amplicon sequencing results indicated that the alpha diversity indices were not affected by the HC feeding. At the phylum level, the milk bacteria were dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes both in the CON and HC groups. At the genus level, the HC cows displayed an improved proportion of Labrys (P = 0.015) compared with the CON cows. Results of both the principal components analysis and partial least squares of discriminant analysis of milk metabolome revealed that samples of the CON and HC groups clustered separately. A total of 31 differential metabolites were identified between the two groups. Of these, the levels of 11 metabolites decreased (α-linolenic acid, prostaglandin E2, L-lactic acid, L-malic acid, 3-hydroxysebacic acid, succinyladenosine, guanosine, pyridoxal, L-glutamic acid, hippuric acid, and trigonelline), whereas the levels of the other 20 metabolites increased in the HC group with respect to the CON group (P < 0.05). CONCLUSION These results suggested that subacute ruminal acidosis less impacted the diversity and composition of milk microbiota, but altered the milk metabolic profiles, which led to the decline of the milk quality.
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Affiliation(s)
- Yingyu Mu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangpan Qi
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiyou Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, 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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Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods. PLoS One 2022; 17:e0267992. [PMID: 36107863 PMCID: PMC9477292 DOI: 10.1371/journal.pone.0267992] [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: 04/15/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine bulk milk, we assembled and tested a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. The following protocol variations were examined:: BCMC enumeration (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 104 cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. Cell lysis procedures conferred the greatest changes to milk microbiota composition and these effects were confirmed to provide similar results for commercial milk samples. Overall, our systematic approach with the BCMC is broadly applicable to other milk, food, and environmental samples therefore recommended for improving accuracy of culture-independent, DNA sequence-based analyses of microbial composition in different habitats.
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Steinberg RS, Silva E Silva LC, de Souza MR, Reis RB, da Silva PCL, Lacorte GA, Nicoli JR, Neumann E, Nunes ÁC. Changes in bovine milk bacterial microbiome from healthy and subclinical mastitis affected animals of the Girolando, Gyr, Guzera, and Holstein breeds. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:803-815. [PMID: 35838927 DOI: 10.1007/s10123-022-00267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 10/17/2022]
Abstract
Raw milk samples were collected from 200 dairy cows belonging to Girolando 1/2, Gyr, Guzera, and Holstein breeds, and the bacterial diversity was explored using 16S rRNA amplicon sequencing. SCC analysis showed that 69 animals were classified as affected with subclinical mastitis. The milk bacterial microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with an increase of Firmicutes in animals with subclinical mastitis and Proteobacteria in healthy animals. At the family and genus level, the milk bacterial microbiome was dominated by Staphylococcus, Acinetobacter, Pseudomonas, members of the family Enterobacteriaceae, Lactococcus, Aerococcus, members of the family Rhizobiaceae, Anaerobacillus, Streptococcus, members of the family Intrasporangiaceae, members of the family Planococcaceae, Corynebacterium, Nocardioides, and Chryseobacterium. Significant differences in alpha and beta diversity analysis suggest an effect of udder health status and breed on the composition of raw bovine milk microbiota. LEfSe analysis showed 45 and 51 discriminative taxonomic biomarkers associated with udder health status and with one of the four breeds respectively, suggesting an effect of subclinical mastitis and breed on the microbiota of milk in cattle.
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Affiliation(s)
- Raphael S Steinberg
- Instituto Federal de Educação Ciência e Tecnologia de Minas Gerais, Campus Bambuí, Rodovia Bambuí/Medeiros - km 05, Caixa Postal 05, Bambuí, MG, 38900-000, Brazil.
| | - Lilian C Silva E Silva
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcelo R de Souza
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Universidade Federal de Minas Gerais, MG, Belo Horizonte, Brazil
| | - Ronaldo B Reis
- Departamento de Zootecnia, Universidade Federal de Minas Gerais, MG, Belo Horizonte, Brazil
| | - Patrícia C L da Silva
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gustavo A Lacorte
- Instituto Federal de Educação Ciência e Tecnologia de Minas Gerais, Campus Bambuí, Rodovia Bambuí/Medeiros - km 05, Caixa Postal 05, Bambuí, MG, 38900-000, Brazil
| | - Jacques R Nicoli
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Elisabeth Neumann
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Álvaro C Nunes
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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10
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Dean CJ, Peña-Mosca F, Ray T, Heins BJ, Machado VS, Pinedo PJ, Caixeta LS, Noyes NR. Evaluation of Contamination in Milk Samples Pooled From Independently Collected Quarters Within a Laboratory Setting. Front Vet Sci 2022; 9:818778. [PMID: 35782536 PMCID: PMC9244618 DOI: 10.3389/fvets.2022.818778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/20/2022] [Indexed: 12/01/2022] Open
Abstract
The primary objective of this observational study was to evaluate the prevalence of contamination from independently collected quarter-level milk samples pooled in a laboratory and subjected to bacterial culture. To address this objective, weekly quarter-level milk samples were collected longitudinally from a cohort of 503 primiparous cows from five organic dairy farms during the first 5 weeks after calving. Individual quarter milk samples were pooled in a laboratory using aseptic technique (“lab-pooled”) and subjected to bacterial culture. In the sample set of 2,006 lab-pooled milk samples, 207 (10.3%) were classified as contaminated using a standard definition (i.e., growth of three or more distinct microorganisms). Subsequent culturing of corresponding quarter-level milk samples revealed that many of the contaminated lab-pooled sample results (i.e., 46.7%) were the result of intramammary infections with different pathogens across the quarters, rather than actual contamination within any single quarter (i.e., “true contamination”). The odds of true contamination were lower when the lab-pooled sample exhibited growth of three microorganisms compared to more than 3 microorganisms. Our findings suggest that pooling of quarter samples within a laboratory setting may yield lower rates of contamination compared to those previously reported from samples composited on-farm, but that current cut-offs to define contamination may need to be evaluated for use with lab-pooled samples. Further investigation of use of lab-pooled samples may be warranted to reduce costs while still providing useful scientific insight.
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Affiliation(s)
- Chris J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Felipe Peña-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Tui Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Bradley J. Heins
- Department of Animal Science, University of Minnesota, St. Paul, MN, United States
| | - Vinicius S. Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pablo J. Pinedo
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Luciano S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
- *Correspondence: Noelle R. Noyes
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11
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Winther AR, Narvhus JA, Smistad M, da Silva Duarte V, Bombelli A, Porcellato D. Longitudinal dynamics of the bovine udder microbiota. Anim Microbiome 2022; 4:26. [PMID: 35395785 PMCID: PMC8994269 DOI: 10.1186/s42523-022-00177-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, the number of studies concerning microbiota of the intramammary environment has increased rapidly due to the development of high-throughput sequencing technologies that allow mapping of microbiota without culturing. This has revealed that an environment previously thought to be sterile in fact harbours a microbial community. Since this discovery, many studies have investigated the microbiota of different parts of the udder in various conditions. However, few studies have followed the changes that occur in the udder microbiota over time. In this study, the temporal dynamics of the udder microbiota of 10 cows, five with a low somatic cell count (SCC, SCC < 100,000 cells/mL) and five with a high SCC (SCC > 100,000 cells/mL), were followed over 5 months to gather insights into this knowledge gap. RESULTS Analysis of the temporal changes in the microbial composition of milk from udders with a low SCC revealed a dynamic and diverse microbiota. When an imbalance due to one dominating genus was recorded, the dominant genus quickly vanished, and the high diversity was restored. The genera dominating in the samples with a high SCC remained the dominant genera throughout the whole sampling period. These cows generally displayed a heightened SCC or an intramammary infection in at least one quarter though-out the sampling period. CONCLUSION Our results show that the bovine udder has a diverse microbiota, and that the composition and diversity of this community affects udder health with regards to SCC. Understanding what influences the composition and stability of this community has important implications for the understanding, control, and treatment of mastitis.
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Affiliation(s)
- Anja Ruud Winther
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, Ås, Norway.
| | - Judith A Narvhus
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, Ås, Norway
| | - Marit Smistad
- Norwegian Veterinary Institute, Oslo, Norway.,TINE SA, Oslo, Norway
| | - Vinicius da Silva Duarte
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, Ås, Norway
| | - Alberto Bombelli
- Department of Agrotechnology and Food Science, Wageningen University and Research, Wageningen, Netherlands
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, Ås, Norway
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12
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Ruegg PL. The bovine milk microbiome - an evolving science. Domest Anim Endocrinol 2022; 79:106708. [PMID: 35038617 DOI: 10.1016/j.domaniend.2021.106708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/21/2022]
Abstract
Improved access to genome based, culture independent methods has generated great interest in defining the bovine milk microbiome. Several comprehensive reviews of this subject have recently been published and the purpose of this short review is to consolidate current understanding of the relevance and biological significance of this emerging topic. In contrast to mucosal organs that contain rich and well-characterized culturable and nonculturable microbial communities, milk obtained from the healthy bovine mammary gland usually contains few or no viable bacteria. The low bacterial biomass of milk has created methodological challenges that have resulted in considerable variability in results of studies that have used genomic methods to define the microbiota of milk obtained from healthy or diseased mammary glands. While genomes from several bacterial genera are routinely identified from samples of milk, teat skin and the teat canal, the viability, origin, and function of these organisms is uncertain as environmental factors have been shown to strongly influence the composition of these bacterial populations. Possible sources of microbial DNA include bacteria introduced from skin or the environment, bacteria trapped in teat canal keratin or bacteria engulfed by phagocytes. Researchers have not achieved consensus about key concepts such as the presence of a core commensal milk microbiome or dysbiosis as part of a causal pathway disrupting udder health. Understanding of the bovine milk microbiome has been greatly impeded by a lack of standardized methods used to collect, process, and assess bovine milk samples. Sample collection is a critical first step that will determine the validity of results. To minimize contamination with external sources of bacterial DNA, teat sanitation methods used for collection of milk samples that will be subjected to extraction and amplification of bacteria DNA should far exceed aseptic techniques used for collection of milk samples that will be submitted for microbiological culture. A number of laboratory issues have yet to be resolved. Contamination of low biomass samples with bacterial DNA from laboratory reagents is a well-known issue that has affected results of studies using bovine milk samples and results of sequencing of negative controls should always be reported. Replication of experiments has rarely been performed and consistency in results are lacking. While progress has been made, standardization of methods and replication using samples originating from differing farm conditions are critically needed to solidify knowledge of this emerging topic.
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Affiliation(s)
- Pamela L Ruegg
- Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, E. Lansing, MI 48824, USA.
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13
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Schwenker JA, Friedrichsen M, Waschina S, Bang C, Franke A, Mayer R, Hölzel CS. Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples. Microbiologyopen 2022; 11:e1275. [PMID: 35478279 PMCID: PMC9059235 DOI: 10.1002/mbo3.1275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 01/04/2023] Open
Abstract
The use of an adequate protocol that accurately extracts microbial DNA from bovine milk samples is of importance for downstream analysis such as 16S ribosomal RNA gene sequencing. Although sequencing platforms such as Illumina are very common, there are reservations concerning reproducibility in challenging samples that combine low bacterial loads with high amounts of host DNA. The objective of this study was to evaluate six different DNA extraction protocols applied to four different prototype milk samples (low/high level of colony‐forming units [cfu] and somatic cells). DNA extracts were sequenced on Illumina MiSeq with primers for the hypervariable regions V1V2 and V3V4. Different protocols were evaluated by analyzing the yield and purity of DNA extracts and the number of clean reads after sequencing. Three protocols with the highest median number of clean reads were selected. To assess reproducibility, these extraction replicates were resequenced in triplicates (n = 120). The most reproducible results for α‐ and β‐diversity were obtained with the modified DNeasy Blood & Tissue kit after a chemical pretreatment plus resuspension of the cream fraction. The unmodified QIAamp DNA Mini kit performed particularly weak in the sample representing unspecific mastitis. These results suggest that pretreatment in combination with the modified DNeasy Blood & Tissue kit is useful in extracting microbial DNA from challenging milk samples. To increase reproducibility, we recommend that duplicates, if not triplicates, should be sequenced. We showed that high counts of somatic cells challenged DNA extraction, which shapes the need to apply modified extraction protocols.
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Affiliation(s)
- Julia A. Schwenker
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
| | - Meike Friedrichsen
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Nutriinformatics Christian‐Albrechts‐University Kiel Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University Kiel Germany
| | - Ricarda Mayer
- Department of Veterinary Sciences Ludwig‐Maximilians‐University Munich Oberschleißheim Germany
- GNA Biosolutions GmbH Martinsried Germany
| | - Christina S. Hölzel
- Department for Animal Hygiene and Health, Institute of Animal Breeding and Husbandry Christian‐Albrechts‐University Kiel Germany
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14
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Ray T, Gaire TN, Dean CJ, Rowe S, Godden SM, Noyes NR. The microbiome of common bedding materials before and after use on commercial dairy farms. Anim Microbiome 2022; 4:18. [PMID: 35256016 PMCID: PMC8900318 DOI: 10.1186/s42523-022-00171-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/23/2022] [Indexed: 01/04/2023] Open
Abstract
Background Bovine mastitis is one of the most economically important diseases affecting dairy cows. The choice of bedding material has been identified as an important risk factor contributing to the development of mastitis. However, few reports examine both the culturable and nonculturable microbial composition of commonly used bedding materials, i.e., the microbiome. Given the prevalence of nonculturable microbes in most environments, this information could be an important step to understanding whether and how the bedding microbiome acts as a risk factor for mastitis. Therefore, our objective was to characterize the microbiome composition and diversity of bedding material microbiomes, before and after use.
Methods We collected 88 bedding samples from 44 dairy farms in the U.S. Unused (from storage pile) and used (out of stalls) bedding materials were collected from four bedding types: new sand (NSA), recycled manure solids (RMS), organic non-manure (ON) and recycled sand (RSA). Samples were analyzed using 16S rRNA sequencing of the V3–V4 region. Results The overall composition as well as the counts of several microbial taxa differed between bedding types, with Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes dominating across all types. Used bedding contained a significantly different microbial composition than unused bedding, but the magnitude of this difference varied by bedding type, with RMS bedding exhibiting the smallest difference. In addition, positive correlations were observed between 16S rRNA sequence counts of potential mastitis pathogens (bacterial genera) and corresponding bedding bacterial culture data. Conclusion Our results strengthen the role of bedding as a potential source of mastitis pathogens. The consistent shift in the microbiome of all bedding types that occurred during use by dairy cows deserves further investigation to understand whether this shift promotes pathogen colonization and/or persistence, or whether it can differentially impact udder health outcomes. Future studies of bedding and udder health may be strengthened by including a microbiome component to the study design. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00171-2.
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15
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Li P, Fu T, Cai A, Descovich K, Lian H, Gao T, Phillips CJC. Effect of Peanut Shell and Rice Husk Bedding for Dairy Cows: An Analysis of Material Properties and Colostrum Microbiota. Animals (Basel) 2022; 12:ani12050603. [PMID: 35268172 PMCID: PMC8909170 DOI: 10.3390/ani12050603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The provision of appropriate bedding is important for the welfare of dairy cows. Before bedding can be selected, it is critical to understand the properties of the bedding, including its impact on milk microbiota. The objective of this article was to evaluate the influence of three materials for use as bedding on physicochemical properties, bacterial counts and colostrum microbiota of cows. Our results demonstrate that peanut shells appear to be a suitable bedding material for cows. These experiments provide empirical support for the use of peanut shells and rice husks as bedding material for dairy cows and illustrates the effects of bedding types on the colostrum microbiota of dairy cows. Abstract The aim of this study was to evaluate peanut shells and rice husks as bedding for dairy cows. We analyzed material properties including dry matter, water holding capacity, pH level and bacterial counts. Bedding treatments were compared with a one-way ANOVA using twelve cows split into three groups. Colostrum microbiota was analyzed by sequencing of the V3–V4 region of the 16S rRNA gene. Dry matter content was higher in rice husks compared with peanut shells. No treatment effects were found for water holding capacity and pH level. Streptococcus agalactia counts in peanut shell bedding were lower than in rice husk bedding, and Pseudomonas aeruginosa counts were not different between beddings. A significant enrichment for Enhydrobacter and Pantoea were detected in the colostrum of cows that used peanut shells compared with other beddings. Colostrum of cows housed on a peanut–rice combination had a greater relative abundance of Pseudomonas and Corynebacterium than those housed on peanut shells or rice husks. Higher numbers of Bacteroides, Akkermansia, Alistipes, Ruminococcaceae_UCG-014, Coriobacteriaceae_UCG-002 and Intestinimona were found in the colostrum of cows housed on rice husk bedding over other bedding types. These results suggest that bedding types were associated with the growth and diversity of colostrum bacterial loads. In addition, dry matter in peanut shells was lower than found in rice husks, but there was also a lower risk of mastitis for peanut shell bedding than other beddings.
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Affiliation(s)
- Pengtao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (P.L.); (T.F.); (A.C.); (H.L.)
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (P.L.); (T.F.); (A.C.); (H.L.)
| | - Amin Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (P.L.); (T.F.); (A.C.); (H.L.)
| | - Kris Descovich
- Center for Animal Welfare and Ethics, School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia;
| | - Hongxia Lian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (P.L.); (T.F.); (A.C.); (H.L.)
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (P.L.); (T.F.); (A.C.); (H.L.)
- Correspondence: (T.G.); (C.J.C.P.)
| | - Clive J. C. Phillips
- Center for Animal Welfare and Ethics, School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia;
- Sustainable Policy (CUSP) Institute, Curtin University, Bentley, WA 6102, Australia
- Correspondence: (T.G.); (C.J.C.P.)
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16
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Shinozuka Y, Suzuki N, Kaneko S, Kawai K, Kurumisawa T, Shimizu Y, Imanishi T, Ohno A, Takahashi M, Isobe N. Regression tree analysis of the relationship between the concentrations of antimicrobial components and the microbiota of normal milk from dairy cows. J Vet Med Sci 2022; 84:310-318. [PMID: 35046240 PMCID: PMC8983300 DOI: 10.1292/jvms.21-0541] [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] [Indexed: 11/22/2022] Open
Abstract
The purpose of this study was to determine the concentrations of antimicrobial components (immunoglobulin A (IgA), lactoferrin (LF), lingual antimicrobial peptide (LAP), and S100A7) in normal milk and their relation to host factors (Age, somatic cell count (SCC), days in milk, richness, and alpha diversity of the milk microbiota) in dairy cows using multivariate regression tree analyses, and to clarify how the milk microbiota is related to the obtained results. Thirty normal milk samples were collected from a commercial dairy farm in June 2020. The thresholds that predicted the concentration of each antimicrobial component in milk were obtained by regression tree analysis, and the beta-diversity of the milk microbiota composition between groups divided according to each threshold was compared by an analysis of similarities test. The IgA and LF concentrations were mainly predicted by the SCC (177,500 and 70,000 cells/ml, respectively), and the LAP and S100A7 concentrations were predicted by Age (29.667 and 40.3 months, respectively). No relationship was observed between the concentration of IgA, LAP, or S100A7 and the milk microbiota composition between the groups divided by the threshold for prediction, but the milk microbiota composition was significantly different between the groups divided by the threshold for predicting the LF concentration. Our results indicated that the LF concentration in normal milk may be associated with the milk microbiota composition.
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Affiliation(s)
- Yasunori Shinozuka
- School of Veterinary Medicine, Azabu University.,Azabu University Mastitis Research Center
| | - Naoki Suzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | | | - Kazuhiro Kawai
- School of Veterinary Medicine, Azabu University.,Azabu University Mastitis Research Center
| | - Tomomi Kurumisawa
- School of Veterinary Medicine, Azabu University.,Azabu University Mastitis Research Center
| | | | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Ayumu Ohno
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Mano Takahashi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Naoki Isobe
- Graduate School of Integrated Sciences for Life, Hiroshima University
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17
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Shinozuka Y, Kawai K, Kurumisawa T, Shimizu Y, Imanishi T, Ohno A, Takahashi M, Kaneko S, Suzuki N. Examination of the microbiota of normal cow milk using MinION TM nanopore sequencing. J Vet Med Sci 2021; 83:1620-1627. [PMID: 34526421 PMCID: PMC8636880 DOI: 10.1292/jvms.21-0353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to evaluate the microbiota of normal milk in dairy cows and their relationship with host factors, such as the age of the cow (Age), somatic cell counts in milk
(SCCs), and days in milk (DIM). We investigated 48 milk samples from 22 cows with no systemic or local clinical signs using MinIONTM nanopore sequencing for a 16S
rRNA gene amplicon. Bacterial richness was positively correlated with the DIM (P=0.043), and both the Shannon-Wiener Index and Simpson’s Index, which are metrics
of alpha-diversity, were also significantly positively correlated with the SCC (P<0.001). The composition ratios of both Actinobacteria at the phylum level and
Kocuria spp. at the genus level in the milk microbiota were significantly correlated with the SCC (P<0.001 and P<0.001,
respectively). In the beta-diversity test, the one-way analysis of similarities test showed a significant difference (P=0.0051) between the low- and high-SCC groups. This
study clarified that the composition of the normal milk microbiota in this herd was related to the SCC. It also raised the possibility of variations in bacterial genera in the normal milk
microbiota between the low- and high-SCC groups. However, to clarify the actual condition of the milk microbiota and to elucidate the relationship with the SCC, it is necessary to perform
further analyses taking into account not only the relative abundance, but also the absolute abundance of microbes.
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Affiliation(s)
- Yasunori Shinozuka
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan.,Azabu University Mastitis Research Center, Sagamihara, Kanagawa 252-5201, Japan
| | - Kazuhiro Kawai
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan.,Azabu University Mastitis Research Center, Sagamihara, Kanagawa 252-5201, Japan
| | - Tomomi Kurumisawa
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan.,Azabu University Mastitis Research Center, Sagamihara, Kanagawa 252-5201, Japan
| | - Yuko Shimizu
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Ayumu Ohno
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Mano Takahashi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Sohei Kaneko
- Higashi-Hiroshima Veterinary Clinical Center, Higashi-Hiroshima, Hiroshima 739-2106, Japan
| | - Naoki Suzuki
- Higashi-Hiroshima Veterinary Clinical Center, Higashi-Hiroshima, Hiroshima 739-2106, Japan.,Present address: Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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18
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Ma T, Shen L, Wen Q, Lv R, Hou Q, Kwok LY, Sun Z, Zhang H. PacBio sequencing revealed variation in the microbiota diversity, species richness and composition between milk collected from healthy and mastitis cows. MICROBIOLOGY-SGM 2021; 167. [PMID: 34292863 DOI: 10.1099/mic.0.000968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mastitis is the economically most important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length 16S rRNAs from 27 milk samples (18 from mastitis and nine from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota of different groups also varied greatly. The healthy cow milk microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii, and Bacteroides dorei, while the milk from mastitis cows was predominantly comprised of Bacillus cereus. The prevalence of L. lactis and B. cereus in the milk samples was confirmed by digital droplets PCR. Differences in the milk microbiota diversity and composition could suggest an important role for some these microbes in protecting the host from mastitis while others associated with mastitis. The results of our research serve as useful references for designing strategies to prevent and treat mastitis.
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Affiliation(s)
- Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lai Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
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19
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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems 2021; 6:e0061921. [PMID: 34128697 PMCID: PMC8574158 DOI: 10.1128/msystems.00619-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. The focus of this study is on gathering the primary material, in this case, DNA. We used bovine milk as a model to (i) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk, (ii) evaluate host DNA depletion methods for use with milk, and (iii) develop and evaluate a selective lysis-propidium monoazide (PMA)-based protocol for host DNA depletion in milk. Our results suggest that magnetically based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting the finding that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety, where the detection of Gram-negative pathogens and hygiene indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. IMPORTANCE Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around 1,000 times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods for the ability to detect specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
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Abellan-Schneyder I, Siebert A, Hofmann K, Wenning M, Neuhaus K. Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk. Microorganisms 2021; 9:1251. [PMID: 34207561 PMCID: PMC8229006 DOI: 10.3390/microorganisms9061251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/02/2022] Open
Abstract
Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.
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Affiliation(s)
- Isabel Abellan-Schneyder
- Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany;
| | - Annemarie Siebert
- Chair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany; (A.S.); (K.H.); (M.W.)
| | - Katharina Hofmann
- Chair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany; (A.S.); (K.H.); (M.W.)
| | - Mareike Wenning
- Chair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany; (A.S.); (K.H.); (M.W.)
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit LGL, 85764 Oberschleißheim, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany;
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Siebert A, Hofmann K, Staib L, Doll EV, Scherer S, Wenning M. Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR. Appl Microbiol Biotechnol 2021; 105:4761-4773. [PMID: 34059942 PMCID: PMC8195793 DOI: 10.1007/s00253-021-11353-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/29/2021] [Accepted: 05/16/2021] [Indexed: 01/12/2023]
Abstract
Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11353-4.
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Affiliation(s)
- Annemarie Siebert
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Katharina Hofmann
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Lena Staib
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Etienne V Doll
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Siegfried Scherer
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mareike Wenning
- Chair of Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleissheim, Germany.
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Nagy Á, Székelyhidi R, Hanczné Lakatos E, Kapcsándi V. Review on the occurrence of the mcr-1 gene causing colistin resistance in cow's milk and dairy products. Heliyon 2021; 7:e06800. [PMID: 33898852 PMCID: PMC8060599 DOI: 10.1016/j.heliyon.2021.e06800] [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: 01/04/2021] [Revised: 02/25/2021] [Accepted: 04/10/2021] [Indexed: 01/17/2023] Open
Abstract
Both livestock farmers and the clinic use significant amount of antibiotics worldwide, in many cases the same kind. Antibiotic resistance is not a new phenomenon, however, it is a matter of concern that resistance genes (mcr - Mobilized Colistin Resistance - genes) that render last-resort drugs (Colistin) ineffective, have already evolved. Nowadays, there is a significant consumption of milk and dairy products, which, if not treated properly, can contain bacteria (mainly Gram-negative bacteria). We collected articles and reviews in which Gram-negative bacteria carrying the mcr-1 gene have been detected in milk, dairy products, or cattle. Reports have shown that although the incidence is still low, unfortunately the gene has been detected in some dairy products on almost every continent. In the interest of our health, the use of colistin in livestock farming must be banned as soon as possible, and new treatments should be applied so that we can continue to have a chance in fighting multidrug-resistant bacteria in human medicine.
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Refining Knowledge of Factors Affecting Vitamin B 12 Concentration in Bovine Milk. Animals (Basel) 2021; 11:ani11020532. [PMID: 33670816 PMCID: PMC7922057 DOI: 10.3390/ani11020532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Milk is considered a staple and complete food that contains several essential nutrients for humans. For instance, it is an excellent natural source of vitamin B12 (B12) due to the presence in the bovine rumen of a myriad of bacteria and archaea capable of producing the vitamin. This vitamin is only produced by prokaryotic microorganisms; vegetal products do not naturally contain it. A 250-mL glass of milk contains about 46% of the daily recommended dietary allowance of B12 for individuals over 13 years old. However, B12 concentration is variable in milk; therefore, identifying factors contributing to its variation is critical to ensure a stable B12 supply for consumers. The aims of these experiments are to gather more knowledge on possible sources of variation in B12 concentrations in milk in order to optimize and stabilize its levels and thereby improve the perception of milk in terms of its health benefits. We observed that B12 concentration increases when the conditions of the rumen are optimal, such as with elevated pH. We also studied if bedding type—e.g., recycled manure solid bedding or straw, which has been reported to impact milk microbiota—could have an impact on milk B12 concentration. In this study, no such correlation was detected. This paper is one of a series seeking to elucidate factors responsible for variations in milk B12 concentration. Abstract Milk is an excellent source of vitamin B12 (B12) for humans. Therefore, being able to guarantee a high and consistent concentration of this vitamin would enhance consumer perception of milk as a health food. The aim of the paper was to gather additional knowledge on factors that could explain B12 variation in cow milk through two observational studies: (1) to explore the relationship between milk B12 and ruminal conditions, such as pH and volatile fatty acid concentrations; and (2) to examine the impact of bedding on B12 concentrations in bulk tank milk. For study 1, a total of 72 milk and ruminal liquid samples were obtained from 45 Holstein cows fitted with ruminal cannula between 10 and 392 days of lactation. For study 2, bulk tank milk samples were obtained from 83 commercial herds; 26 herds used recycled manure solid bedding and 57 used straw bedding. Milk samples were analyzed for B12 using radioassay. Using principal component regression analysis, we observed that ruminal pH and the acetate:propionate ratio for cows receiving the early lactation ration were positively correlated with milk B12. Bedding did not influence milk B12 in bulk tanks, which averaged 4276 pg/mL. In conclusion, as B12 is synthesized by ruminal bacteria, optimizing ruminal conditions had a positive effect on milk B12, while bedding management had no influence.
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A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis. Sci Rep 2020; 10:21608. [PMID: 33303769 PMCID: PMC7729973 DOI: 10.1038/s41598-020-77054-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
The importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.
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Guzmán-Rodríguez JJ, León-Galván MF, Barboza-Corona JE, Valencia-Posadas M, Loeza-Lara PD, Sánchez-Ceja M, Ochoa-Zarzosa A, López-Meza JE, Gutiérrez-Chávez AJ. Analysis of virulence traits of Staphylococcus aureus isolated from bovine mastitis in semi-intensive and family dairy farms. J Vet Sci 2020; 21:e77. [PMID: 33016022 PMCID: PMC7533384 DOI: 10.4142/jvs.2020.21.e77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/21/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Staphylococcus aureus is one of the main microorganisms that causes bovine mastitis, and its well-known virulence characteristics and interactions with the environment are used to aid the design of more efficient therapies. OBJECTIVES To determine whether the virulence traits, such as antibiotic resistance and biofilm-forming and internalization abilities, of S. aureus isolated from bovine mastitis are related to dairy production system types. METHODS The study was performed in the Mexican states of Guanajuato and Michoacan. Semi-intensive dairy farms (SIDFs) and family dairy farms (FDFs) (454 and 363 cows, respectively) were included. The 194 milk samples from mastitis affected quarters were collected and 92 strains of S. aureus were isolated and identified by biochemical and molecular tests. Antibiotic resistance, biofilm and internalization assays were performed on 30 randomly selected isolated strains to determine virulence traits, and these strains were equally allocated to the 2 dairy production systems. RESULTS All 30 selected strains displayed a high degree of resistance (50%-91.7%) to the antibiotics tested, but no significant difference was found between SIDF and FDF isolates. S. aureus strains from SIDFs had an average biofilm forming capacity of up to 36% (18.9%-53.1%), while S. aureus strains from FDFs registered an average of up to 53% (31.5%-77.8%) (p > 0.05). Internalization assays revealed a higher frequency of internalization capacity for strains isolated from FDFs (33.3%) than for those isolated from SIDFs (6.7%) (p > 0.05). fnbpA gen was detected in 46.6% of FDF strains and 33.3% of SIDF strains, and this difference was significant (p < 0.05). CONCLUSIONS Our findings show that the virulence traits of S. aureus isolates analyzed in this study, depend significantly on several factors, such as phenotype, genotype, and environmental conditions, which are significantly related to dairy production system type and daily management practices.
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Affiliation(s)
- Jaquelina J Guzmán-Rodríguez
- Life Science Division, Postgraduate Program in Bioscience, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
| | - Ma Fabiola León-Galván
- Life Science Division, Postgraduate Program in Bioscience, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
- Life Science Division, Department of Food, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
| | - José E Barboza-Corona
- Life Science Division, Postgraduate Program in Bioscience, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
- Life Science Division, Department of Food, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
| | - Mauricio Valencia-Posadas
- Life Science Division, Postgraduate Program in Bioscience, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
- Life Science Division, Department of Veterinary Medicine and Zootechnics, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
| | - Pedro D Loeza-Lara
- Department of Food Genomics, University of La Cienega of the State of Michoacan de Ocampo, 59103 Sahuayo, Michoacan, Mexico
| | - Mónica Sánchez-Ceja
- Department of Food Genomics, University of La Cienega of the State of Michoacan de Ocampo, 59103 Sahuayo, Michoacan, Mexico
| | - Alejandra Ochoa-Zarzosa
- Multidisciplinary Center for Biotechnology Studies, Faculty of Veterinary Medicine and Zootechnics, Universidad Michoacana de San Nicolas de Hidalgo, 58893 Morelia, Michoacán, Mexico
| | - Joel E López-Meza
- Multidisciplinary Center for Biotechnology Studies, Faculty of Veterinary Medicine and Zootechnics, Universidad Michoacana de San Nicolas de Hidalgo, 58893 Morelia, Michoacán, Mexico
| | - Abner J Gutiérrez-Chávez
- Life Science Division, Postgraduate Program in Bioscience, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico
- Life Science Division, Department of Veterinary Medicine and Zootechnics, Irapuato-Salamanca Campus, University of Guanajuato, 36500 Irapuato, Guanajuato, Mexico.
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Ismail ZB, Abutarbush SM. Molecular characterization of antimicrobial resistance and virulence genes of Escherichia coli isolates from bovine mastitis. Vet World 2020; 13:1588-1593. [PMID: 33061231 PMCID: PMC7522938 DOI: 10.14202/vetworld.2020.1588-1593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/22/2020] [Indexed: 01/09/2023] Open
Abstract
Background and Aim: Mastitis is a common and economically important disease in dairy cattle. It remains one of the most common reasons for the extensive use of antimicrobials in dairy farms leading to the emergence of antimicrobial-resistant pathogens. The aim of this study was to determine the patterns of antimicrobial resistance of Escherichia coli isolates from bovine mastitis and to identify prominent antimicrobial resistance and virulence genes among isolated strains. Materials and Methods: Antimicrobial susceptibility testing against six antibiotic groups, including tetracyclines, aminoglycosides, beta-lactams, macrolides, sulfonamides, and fluoroquinolones was performed using the disk diffusion method. PCR was performed on resistant isolates to detect resistance and virulence genes using commercially available primers. Results: Out of 216 milk samples cultured, 14 samples yielded E. coli isolates. All isolates (100%) were resistant to ampicillin, amoxicillin, procaine penicillin, streptomycin, oxytetracycline, and sulfamethoxazole-trimethoprim. Only one isolate (7%) was sensitive to gentamicin, and all isolates (100%) were sensitive to enrofloxacin and ciprofloxacin. All isolates carried at least one resistance gene against one or more of the major antibiotic groups. All isolates carried the ereA, tetG, tetE, and tetB genes, followed by tetA (93%), ampC (86%), strA (86%), sul1 (78%), tetD (71%), tetC (57%), aadA (57%), and strB (36%). The lowest percentage of isolates carried bla1 (17%) and bla2 (12%) genes, and none of the isolates carried the qnrA gene. Most of the isolates (93%) carried the Shiga toxin 1 virulence gene, followed by complement resistance protein (79%), intimin (64%), Shiga toxin 2 (36%), cytotoxic necrotizing factor (35%), aerotaxis receptor (21%), and type 1 fimbriae (15%). Conclusion: Results of this study indicate that the high percentages of E. coli isolate from bovine mastitis are resistant to two or more of the major antibiotic groups, irrespective of the presence or absence of relevant resistance or virulence genes.
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Affiliation(s)
- Zuhair Bani Ismail
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Sameeh M Abutarbush
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
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Witzke MC, Gullic A, Yang P, Bivens NJ, Adkins PRF, Ericsson AC. Influence of PCR cycle number on 16S rRNA gene amplicon sequencing of low biomass samples. J Microbiol Methods 2020; 176:106033. [PMID: 32805370 DOI: 10.1016/j.mimet.2020.106033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
The objective of this study was to evaluate the effects of increased PCR cycle number on sequencing results from samples with low microbial biomass, including bovine milk, and murine pelage and blood. We hypothesized that subjecting DNA from such samples to higher PCR cycle numbers would increase 16S rRNA sequencing coverage. DNA was extracted from matched samples of each type and multiple PCR cycle numbers were evaluated to generate a total of 96 libraries from 24 milk samples, 46 libraries from 23 pelage samples, and 170 libraries from 85 blood samples. 16S rRNA sequencing was performed on the Illumina MiSeq platform, and the coverage per sample, detected richness, and beta-diversity were evaluated. Across all sample types, higher PCR cycle numbers were associated with increased coverage. Surprisingly however, while higher PCR cycle numbers resulted in greater number of useable datapoints, no differences were detected in metrics of richness or beta-diversity. While reagent controls amplified for 40 cycles yielded similarly increased coverage, control and experimental samples were clearly differentiated based on beta-diversity. The results from this study support the use of higher PCR cycle numbers to evaluate samples with low microbial biomass.
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Affiliation(s)
- Monica C Witzke
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Alexis Gullic
- University of Missouri, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Peggy Yang
- University of Michigan, Unit for Laboratory Animal Medicine, Ann Arbor, MI, USA
| | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, USA
| | - Pamela R F Adkins
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Aaron C Ericsson
- University of Missouri, Metagenomics Center (MUMC), Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA.
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29
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Breitenwieser F, Doll EV, Clavel T, Scherer S, Wenning M. Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota. Front Microbiol 2020; 11:1557. [PMID: 32742267 PMCID: PMC7365021 DOI: 10.3389/fmicb.2020.01557] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25–28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.
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Affiliation(s)
| | - Etienne V Doll
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.,ZIEL - Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Mareike Wenning
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany.,Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
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30
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Dahlberg J, Williams JE, McGuire MA, Peterson HK, Östensson K, Agenäs S, Dicksved J, Waller KP. Microbiota of bovine milk, teat skin, and teat canal: Similarity and variation due to sampling technique and milk fraction. J Dairy Sci 2020; 103:7322-7330. [PMID: 32534929 DOI: 10.3168/jds.2019-17783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/07/2020] [Indexed: 01/13/2023]
Abstract
The aim of this study was to evaluate the effect of sampling technique and milk fraction on bovine milk microbiota data and to compare the microbiota in milk to microbiota on the teat end and in the teat canal. Representative milk samples are highly important for assessment of bacteriological findings and microbiota in milk. Samples were obtained from 5 healthy lactating dairy cows at udder quarter level during 1 milking. Swab samples from the teat end and teat canal, and milk samples collected using different techniques and in different milk fractions were included. Milk was collected by hand stripping and through a teat canal cannula before and after machine milking, through a trans-teat wall needle aspirate after milking, and from udder quarter composite milk. The microbiota of the samples was analyzed with sequencing of the V1-V3 region of the 16S rRNA gene. In addition, somatic cell counts and bacterial cultivability were analyzed in the milk samples. Microbiota data were analyzed using multivariate methods, and differences between samples were tested using analysis of similarity (ANOSIM). Differences between samples were further explored via individual studies of the 10 most abundant genera. The microbiota on the teat end, in the teat canal, and in udder quarter composite milk, collected using a milking machine, differed in composition from the microbiota in milk collected directly from the udder quarter. No differences in milk microbiota composition were detected between hand-stripped milk samples, milk samples taken through a teat canal cannula, or milk samples taken as a trans-teat wall needle aspirate before or after milking. We conclude that for aseptic milk samples collected directly from the lactating udder quarter, sampling technique or milk fraction has minor effect on the microbiota composition.
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Affiliation(s)
- J Dahlberg
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
| | - J E Williams
- Department of Animal and Veterinary Science, University of Idaho, Moscow 83844
| | - M A McGuire
- Department of Animal and Veterinary Science, University of Idaho, Moscow 83844
| | - H K Peterson
- Department of Animal and Veterinary Science, University of Idaho, Moscow 83844
| | - K Östensson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - S Agenäs
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - J Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - K Persson Waller
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 75189 Uppsala, Sweden
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31
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Oikonomou G, Addis MF, Chassard C, Nader-Macias MEF, Grant I, Delbès C, Bogni CI, Le Loir Y, Even S. Milk Microbiota: What Are We Exactly Talking About? Front Microbiol 2020; 11:60. [PMID: 32117107 PMCID: PMC7034295 DOI: 10.3389/fmicb.2020.00060] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022] Open
Abstract
The development of powerful sequencing techniques has allowed, albeit with some biases, the identification and inventory of complex microbial communities that inhabit different body sites or body fluids, some of which were previously considered sterile. Notably, milk is now considered to host a complex microbial community with great diversity. Milk microbiota is now well documented in various hosts. Based on the growing literature on this microbial community, we address here the question of what milk microbiota is. We summarize and compare the microbial composition of milk in humans and in ruminants and address the existence of a putative core milk microbiota. We discuss the factors that contribute to shape the milk microbiota or affect its composition, including host and environmental factors as well as methodological factors, such as the sampling and sequencing techniques, which likely introduce distortion in milk microbiota analysis. The roles that milk microbiota are likely to play in the mother and offspring physiology and health are presented together with recent data on the hypothesis of an enteromammary pathway. At last, this fascinating field raises a series of questions, which are listed and commented here and which open new research avenues.
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Affiliation(s)
- Georgios Oikonomou
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | | | | | - I Grant
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Celine Delbès
- Université Clermont Auvergne, INRAE, UMRF, Aurillac, France
| | - Cristina Inés Bogni
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Yves Le Loir
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
| | - Sergine Even
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
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Andrews T, Neher DA, Weicht TR, Barlow JW. Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status. PLoS One 2019; 14:e0225001. [PMID: 31725757 PMCID: PMC6855453 DOI: 10.1371/journal.pone.0225001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022] Open
Abstract
Infections of the cow udder leading to mastitis and reducing milk quality are a critical challenge facing all dairy farmers. Mastitis may be linked to the ecological disruption of an endogenous mammary microbial community, suggesting an ecosystems approach to management and prevention of this disease. The teat end skin represents a first point of host contact with mastitis pathogens and may offer an opportunity for microbially mediated resistance to infection, yet we know little about the microbial community of teat end skin or its potential interaction with the microbial community of intramammary milk of organic dairy cattle. High-throughput sequencing of marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected gland (i.e., udder quarter) and to assess the sharing of microbial DNA between these tissue habitat sites. The mammary microbiome varied among cows, through time, and between skin and milk. Microbiomes of milk from healthy and infected quarters reflected a diverse group of microbial DNA sequences, though milk had far fewer operational taxonomic units (OTUs) than skin. Milk microbiomes of infected quarters were generally more variable than healthy quarters and were frequently dominated by a single OTU; teat end skin microbiomes were relatively similar between healthy and infected quarters. Commonly occurring genera that were shared between skin and milk of infected glands included Staphylococcus spp. bacteria and Debaryomyces spp. fungi. Commonly occurring genera that were shared between skin and milk of healthy glands included bacteria SMB53 (Clostridiaceae) and Penicillium spp. fungi. Results support an ecological interpretation of the mammary gland and the notion that mastitis can be described as a dysbiosis, an imbalance of the healthy mammary gland microbiome.
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Affiliation(s)
- Tucker Andrews
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
| | - Deborah A. Neher
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
| | - Thomas R. Weicht
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, United States of America
| | - John W. Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
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Souza FN, Sanchez EM, Della Libera AM, Heinemann MB. Letters to the editor: A comment on “Control of bovine mastitis in the 21st century: Immunize or tolerate?”. Res Vet Sci 2019; 126:20-21. [DOI: 10.1016/j.rvsc.2019.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 06/14/2019] [Accepted: 08/05/2019] [Indexed: 01/09/2023]
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Relationship Between mRNA of Immune Factors Expressed by Milk Somatic Cells and Bacteria Present in Healthy Lactating Holstein Cows. J Vet Res 2019; 63:369-373. [PMID: 31572817 PMCID: PMC6749727 DOI: 10.2478/jvetres-2019-0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022] Open
Abstract
Introduction The characteristics of immune factors in somatic cells from lactating dairy cows and their association with commensal bacteria in normal milk have not been clarified. This study investigated the relationship between the pathogenic bacteria in milk and somatic cell immune factors in healthy lactating cows. Material and Methods In total 44 healthy Holstein cows were studied on one farm. Milk samples were collected aseptically using a cannula and these samples were cultured for detection of bacteria and analysis of mRNA of immune factors expressed by somatic cells. Cows were divided into two groups based on the microbial status of their milk samples: 12 cows showed bacteria in cultures (positive group), and the other 32 cows did not (negative group). Results The mRNA levels of IL-6, lactotransferrin, and cathelicidin expressed by somatic cells after milking decreased significantly compared to those before milking in both groups (P < 0.05). There were significantly lower mRNA levels of IL-6 and cathelicidin in the positive group compared to those in the negative group before milking. Conclusion These results suggest that mRNA levels of IL-6 and cathelicidin expressed by the somatic cells may be affected by the presence of bacteria in healthy lactating dairy cows.
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Amadori M, Addis MF, Bronzo V, Castiglioni B, Moroni P, Piccinini R. A reply to the comment on "control of bovine mastitis in the 21st century: Immunize or tolerize?" by Fernando N. Souza and co-workers. Res Vet Sci 2019; 126:1-3. [PMID: 31415927 DOI: 10.1016/j.rvsc.2019.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Affiliation(s)
- M Amadori
- Laboratory of Animal Welfare, Clinical Chemistry and Veterinary Immunology, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy.
| | - M F Addis
- Università degli Studi di Milano, Department of Veterinary Medicine, Milan, Italy
| | - V Bronzo
- Università degli Studi di Milano, Department of Veterinary Medicine, Milan, Italy
| | - B Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - P Moroni
- Università degli Studi di Milano, Department of Veterinary Medicine, Milan, Italy
| | - R Piccinini
- Università degli Studi di Milano, Department of Veterinary Medicine, Milan, Italy
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Castro I, Alba C, Aparicio M, Arroyo R, Jiménez L, Fernández L, Arias R, Rodríguez JM. Metataxonomic and immunological analysis of milk from ewes with or without a history of mastitis. J Dairy Sci 2019; 102:9298-9311. [PMID: 31421883 DOI: 10.3168/jds.2019-16403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/18/2019] [Indexed: 01/16/2023]
Abstract
Mastitis is a highly prevalent condition that has a great impact on milk production and animal welfare, and often requires substantial management efforts. For this reason, it is generally considered an important threat to the dairy industry. Many microbial, host, and environmental factors can protect against, predispose to, or influence the development of mastitis. The objective of this work was to characterize the milk microbiota of Manchega ewes, and to compare samples from animals with and without a history of mastitis. We analyzed milk samples from 36 ewes belonging to 2 different farms (18 ewes from each farm) using culture-dependent and culture-independent techniques. We also analyzed several immune compounds to investigate associations of mastitis with 3 main variables: farm; history of mastitis or no mastitis; and parity number. Both culture-dependent and culture-independent techniques showed that ewe milk harbored a site-specific complex microbiota and microbiome. Staphylococcus epidermidis was the main species driving the difference between farm A (where it was the dominant species) and B (where it was not). In contrast, samples from farm B were characterized by the presence of a wide spectrum of other coagulase-negative staphylococci. Some of these species have already been associated with subclinical intramammary infections in ruminants. Of the 10 immune compounds assayed in this study, 3 were related to a history of mastitis [IL-8, IFN-γ, and IFN-gamma-induced protein 10 (IP-10)]. Increases in IL-8 concentrations in milk seemed to be a feature of subclinical mastitis in sheep, and in this study, this immune factor was detected only in samples from ewes with some episodes of mastitis and from the group with the highest somatic cell count. We also observed a positive correlation between the samples with the highest somatic cell count and IFN-γ and IP-10 levels. Our results suggest that these 3 compounds could be used as biomarkers for the negative selection of mastitis-prone animals, particularly when somatic cell count is very high.
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Affiliation(s)
- Irma Castro
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain
| | - Claudio Alba
- Departmental Section of Food Technology, Complutense University of Madrid, 28040 Madrid, Spain
| | - Marina Aparicio
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain
| | - Rebeca Arroyo
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain
| | - Lorena Jiménez
- CERSYRA, Regional Institute of Agrifood and Forestry Research and Development of Castilla La Mancha, 13300 Valdepeñas, Spain
| | - Leónides Fernández
- Departmental Section of Food Technology, Complutense University of Madrid, 28040 Madrid, Spain
| | - Ramón Arias
- CERSYRA, Regional Institute of Agrifood and Forestry Research and Development of Castilla La Mancha, 13300 Valdepeñas, Spain.
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain.
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Muletz-Wolz CR, Kurata NP, Himschoot EA, Wenker ES, Quinn EA, Hinde K, Power ML, Fleischer RC. Diversity and temporal dynamics of primate milk microbiomes. Am J Primatol 2019; 81:e22994. [PMID: 31219214 DOI: 10.1002/ajp.22994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/28/2019] [Accepted: 05/05/2019] [Indexed: 12/30/2022]
Abstract
Milk is inhabited by a community of bacteria and is one of the first postnatal sources of microbial exposure for mammalian young. Bacteria in breast milk may enhance immune development, improve intestinal health, and stimulate the gut-brain axis for infants. Variation in milk microbiome structure (e.g., operational taxonomic unit [OTU] diversity, community composition) may lead to different infant developmental outcomes. Milk microbiome structure may depend on evolutionary processes acting at the host species level and ecological processes occurring over lactation time, among others. We quantified milk microbiomes using 16S rRNA high-throughput sequencing for nine primate species and for six primate mothers sampled over lactation. Our data set included humans (Homo sapiens, Philippines and USA) and eight nonhuman primate species living in captivity (bonobo [Pan paniscus], chimpanzee [Pan troglodytes], western lowland gorilla [Gorilla gorilla gorilla], Bornean orangutan [Pongo pygmaeus], Sumatran orangutan [Pongo abelii], rhesus macaque [Macaca mulatta], owl monkey [Aotus nancymaae]) and in the wild (mantled howler monkey [Alouatta palliata]). For a subset of the data, we paired microbiome data with nutrient and hormone assay results to quantify the effect of milk chemistry on milk microbiomes. We detected a core primate milk microbiome of seven bacterial OTUs indicating a robust relationship between these bacteria and primate species. Milk microbiomes differed among primate species with rhesus macaques, humans and mantled howler monkeys having notably distinct milk microbiomes. Gross energy in milk from protein and fat explained some of the variations in microbiome composition among species. Microbiome composition changed in a predictable manner for three primate mothers over lactation time, suggesting that different bacterial communities may be selected for as the infant ages. Our results contribute to understanding ecological and evolutionary relationships between bacteria and primate hosts, which can have applied benefits for humans and endangered primates in our care.
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Affiliation(s)
- Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Naoko P Kurata
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
- The Graduate Center, The City University of New York, New York, New York
- Department of Ichthyology, American Museum of Natural History, New York, New York
| | - Elizabeth A Himschoot
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Elizabeth S Wenker
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Elizabeth A Quinn
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Katie Hinde
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Michael L Power
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
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Murphy SI, Kent D, Martin NH, Evanowski RL, Patel K, Godden SM, Wiedmann M. Bedding and bedding management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk. J Dairy Sci 2019; 102:6885-6900. [PMID: 31202649 DOI: 10.3168/jds.2018-16022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 11/19/2022]
Abstract
Mesophilic and thermophilic spore-forming bacteria represent a challenge to the dairy industry, as these bacteria are capable of surviving adverse conditions associated with processing and sanitation and eventually spoil dairy products. The dairy farm environment, including soil, manure, silage, and bedding, has been implicated as a source for spores in raw milk. High levels of spores have previously been isolated from bedding, and different bedding materials have been associated with spore levels in bulk tank (BT) raw milk; however, the effect of different bedding types, bedding management practices, and bedding spore levels on the variance of spore levels in BT raw milk has not been investigated. To this end, farm and bedding management surveys were administered and unused bedding, used bedding, and BT raw milk samples were collected from dairy farms (1 or 2 times per farm) across the United States over 1 yr; the final data set included 182 dairy farms in 18 states. Bedding suspensions and BT raw milk were spore pasteurized (80°C for 12 min), and mesophilic and thermophilic spores were enumerated. Piecewise structural equation modeling analysis was used to determine direct and indirect pathways of association among farm and bedding practices, levels of spores in unused and used bedding, and levels of spores in BT raw milk. Separate models were constructed for mesophilic and thermophilic spore levels. The analyses showed that bedding material had a direct influence on levels of spores in unused and used bedding as well as an indirect association with spore levels in BT raw milk through used bedding spore levels. Specific bedding and farm management practices as well as cow hygiene in the housing area were associated with mesophilic and thermophilic spore levels in unused bedding, used bedding, and BT raw milk. Notably, levels of spores in used bedding were positively related to those in unused bedding, and used bedding spore levels were positively related to those in BT raw milk. The results of this study increase the understanding of the levels and ecology of mesophilic and thermophilic spores in raw milk, emphasize the possible role of bedding as a source of spores on-farm, and present opportunities for dairy producers to reduce spore levels in BT raw milk.
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Affiliation(s)
- S I Murphy
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - D Kent
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - R L Evanowski
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - K Patel
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul 55108
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul 55108
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
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Taponen S, McGuinness D, Hiitiö H, Simojoki H, Zadoks R, Pyörälä S. Bovine milk microbiome: a more complex issue than expected. Vet Res 2019; 50:44. [PMID: 31171032 PMCID: PMC6555717 DOI: 10.1186/s13567-019-0662-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/13/2019] [Indexed: 01/23/2023] Open
Abstract
The aim of this study was to analyze bacterial profiles of bovine mastitic milk samples and samples from healthy quarters using Next Generation Sequencing of amplicons from 16S rRNA genes and to compare results with microbiological results by PCR assays of the same samples. A total of 49 samples were collected from one single dairy herd during the same day. The samples were divided in two sample sets, which were used in this study. The DNA extraction as well as the library preparation and sequencing of these two sets were performed separately, and results of the two datasets were then compared. The vast majority of genera detected appeared with low read numbers and/or in only a few samples. Results of PCR and microbiome analyses of samples infected with major pathogens Staphylococcus aureus or Streptococcus uberis were consistent as these genera also covered the majority of reads detected in the microbiome analysis. Analysis of alpha diversity revealed a much higher species richness in set 1 than in set 2. The dominating bacterial genera with the highest read numbers clearly differed between datasets, especially in PCR negative samples and samples positive for minor pathogens. In addition to this, linear discriminant analysis (LDA) was conducted between the two sets to identify significantly different genera/family level microbes. The genus Methylobacterium was much more common in set 2 compared to set 1, and genus Streptococcus more common in set 1. Our results indicate amplification of contaminating bacteria in excess in samples with no or minor amounts of pathogen DNA in dataset 2. There is a need for critical assessment of results of milk microbiome analyses.
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Affiliation(s)
- Suvi Taponen
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
| | - David McGuinness
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Heidi Hiitiö
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Heli Simojoki
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ruth Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Satu Pyörälä
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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40
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Abstract
The milk microbiota is an intriguing area of research because milk with no bacterial growth in culture was long thought to be sterile. Recent DNA sequencing techniques have been developed that do not require bacteria to be culturable, and DNA from new bacteria have been reported in milk from dairy cow mammary glands with or without mastitis. Methodologies and results vary among research groups, and not enough is known about the milk microbiota for the results to be used for diagnosis or prognosis of mastitis.
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41
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Vasquez A, Ganda E, Capel M, Eicker S, Virkler P, Bicalho R, Nydam D. The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production. J Dairy Sci 2019; 102:578-594. [DOI: 10.3168/jds.2018-15062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/23/2018] [Indexed: 11/19/2022]
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42
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Alegbeleye OO, Guimarães JT, Cruz AG, Sant’Ana AS. Hazards of a ‘healthy’ trend? An appraisal of the risks of raw milk consumption and the potential of novel treatment technologies to serve as alternatives to pasteurization. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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43
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Cremonesi P, Ceccarani C, Curone G, Severgnini M, Pollera C, Bronzo V, Riva F, Addis MF, Filipe J, Amadori M, Trevisi E, Vigo D, Moroni P, Castiglioni B. Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows. PLoS One 2018; 13:e0205054. [PMID: 30356246 PMCID: PMC6200206 DOI: 10.1371/journal.pone.0205054] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups’ prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7–10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health.
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Affiliation(s)
- Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
- * E-mail:
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
- Dipartimento di Scienze della Salute, San Paolo Hospital Medical School, Università degli Studi di Milano, Milan, Italy
| | - Giulio Curone
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
| | - Claudia Pollera
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Federica Riva
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Joel Filipe
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Massimo Amadori
- Laboratory of Cellular Immunology, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition (DIANA), Facoltà di Scienze Agrarie, Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Daniele Vigo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, United States of America
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
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Pang M, Xie X, Bao H, Sun L, He T, Zhao H, Zhou Y, Zhang L, Zhang H, Wei R, Xie K, Wang R. Insights Into the Bovine Milk Microbiota in Dairy Farms With Different Incidence Rates of Subclinical Mastitis. Front Microbiol 2018; 9:2379. [PMID: 30459717 PMCID: PMC6232673 DOI: 10.3389/fmicb.2018.02379] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Bovine mastitis continues to be a complex disease associated with significant economic loss in dairy industries worldwide. The incidence rate of subclinical mastitis (IRSCM) can show substantial variation among different farms; however, the milk microbiota, which have a direct influence on bovine mammary gland health, have never been associated with the IRSCM. Here, we aimed to use high-throughput DNA sequencing to describe the milk microbiota from two dairy farms with different IRSCMs and to identify the predominant mastitis pathogens along with commensal or potential beneficial bacteria. Our study showed that Klebsiella, Escherichia-Shigella, and Streptococcus were the mastitis-causing pathogens in farm A (with a lower IRSCM), while Streptococcus and Corynebacterium were the mastitis-causing pathogens in farm B (with a higher IRSCM). The relative abundance of all pathogens in farm B (22.12%) was higher than that in farm A (9.82%). However, the genus Bacillus was more prevalent in farm A. These results may be helpful for explaining the lower IRSCM in farm A. Additionally, the gut-associated genera Prevotella, Ruminococcus, Bacteroides, Rikenella, and Alistipes were prevalent in all milk samples, suggesting gut bacteria can be one of the predominant microbial contamination in milk. Moreover, Listeria monocytogenes (a foodborne pathogen) was found to be prevalent in farm A, even though it had a lower IRSCM. Overall, our study showed complex diversity between the milk microbiota in dairy farms with different IRSCMs. This suggests that variation in IRSCMs may not only be determined by the heterogeneity and prevalence of mastitis-causing pathogens but also be associated with potential beneficial bacteria. In the future, milk microbiota should be considered in bovine mammary gland health management. This would be helpful for both the establishment of a targeted mastitis control system and the control of the safety and quality of dairy products.
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Affiliation(s)
- Maoda Pang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xing Xie
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongduo Bao
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lichang Sun
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tao He
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hang Zhao
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Zhou
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lili Zhang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hui Zhang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ruicheng Wei
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kaizhou Xie
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ran Wang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Metzger SA, Hernandez LL, Skarlupka JH, Walker TM, Suen G, Ruegg PL. A Cohort Study of the Milk Microbiota of Healthy and Inflamed Bovine Mammary Glands From Dryoff Through 150 Days in Milk. Front Vet Sci 2018; 5:247. [PMID: 30356776 PMCID: PMC6189514 DOI: 10.3389/fvets.2018.00247] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/17/2018] [Indexed: 01/15/2023] Open
Abstract
The objective of this longitudinal cohort study was to describe the milk microbiota of dairy cow mammary glands based on inflammation status before and after the dry period. Individual mammary quarters were assigned to cohorts based on culture results and somatic cell count (SCC) at dryoff and twice in the first 2 weeks post-calving. Mammary glands that were microbiologically negative and had low SCC (< 100,000 cells/mL) at all 3 sampling periods were classified as Healthy (n = 80). Microbiologically negative mammary glands that had SCC ≥150,000 cells/mL at dryoff and the first post-calving sample were classified as Chronic Culture-Negative Inflammation (CHRON; n = 17). Quarters that did not have both culture-negative milk and SCC ≥ 150,000 cells/mL at dryoff but were culture-negative with SCC ≥ 150,000 at both post-calving sampling periods were classified as Culture-Negative New Inflammation (NEWINF; n = 6). Mammary glands with bacterial growth and SCC ≥ 150,000 cells/mL at all 3 periods were classified as Positive (POS; n = 3). Milk samples were collected from all enrolled quarters until 150 days in milk and subjected to microbiota analysis. Milk samples underwent total DNA extraction, a 40-cycle PCR to amplify the V4 region of the bacterial 16S rRNA gene, and next-generation sequencing. Healthy quarters had the lowest rate of PCR and sequencing success (53, 67, 83, and 67% for Healthy, CHRON, NEWINF, and POS, respectively). Chao richness was greatest in milk collected from Healthy quarters and Shannon diversity was greater in milk from Healthy and CHRON quarters than in milk collected from glands in the NEWINF or POS cohorts. Regardless of cohort, season was associated with both richness and diversity, but stage of lactation was not. The most prevalent OTUs included typical gut- and skin-associated bacteria such as those in the phylum Bacteroidetes and the genera Enhydrobacter and Corynebacterium. The increased sequencing success in quarters with worse health outcomes, combined with the lack of bacterial growth in most samples and the high PCR cycle number required for amplification of bacterial DNA, suggests that the milk microbiota of culture-negative, healthy mammary glands is less abundant than that of culture-negative glands with a history of inflammation.
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Affiliation(s)
- Stephanie A Metzger
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Laura L Hernandez
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph H Skarlupka
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Teresa M Walker
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Pamela L Ruegg
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, United States
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