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Duarte VDS, Porcellato D. Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome. mSphere 2024; 9:e0047023. [PMID: 38054728 PMCID: PMC10826364 DOI: 10.1128/msphere.00470-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Bovine mastitis is a multi-etiological and complex disease, resulting in serious economic consequences for dairy farmers and industry. In recent years, the microbiological evaluation of raw milk has been investigated in-depth using next-generation sequencing approaches such as metataxonomic analysis. Despite this, host DNA is a major concern in the shotgun metagenomic sequencing of microbial communities in milk samples, and it represents a big challenge. In this study, we aimed to evaluate different methods for host DNA depletion and/or microbial DNA enrichment and assess the use of PCR-based whole genome amplification in milk samples with high somatic cell count (SCC) by using short- and long-read sequencing technologies. Our results evidenced that DNA extraction performed differently in terms of host DNA removal, impacting metagenome composition and functional profiles.. Moreover, the ratio of SCC/bacteria ultimately impacts microbial DNA yield, and samples with low SCC (SCC below 100,000 cells/mL) are the most problematic. When milk samples with high SCC (SCC above 200,000 cells/mL) underwent multiple-displacement amplification (MDA), we successfully recovered high-quality metagenome-assembled genomes (MAGs), and long-read sequencing was feasible even for samples with low DNA concentration. By associating MDA and short-read sequencing, we recovered two times more MAGs than in untreated samples, and an ongoing co-infection not reported by traditional methods was detected for mastitis pathogen. Overall, this new approach will improve the detection of mastitis-associated microorganisms and make it possible to examine host-microbiome interactions in bovine mastitis.IMPORTANCENext-generation sequencing technologies have been widely used to gain new insights into the diversity of the microbial community of milk samples and dairy products for different purposes such as microbial safety, profiling of starter cultures, and host-microbiome interactions. Milk is a complex food matrix, and additionally, the presence of host nucleic acid sequences is considered a contaminant in untargeted high-throughput sequencing studies. Therefore, genomic-centric metagenomic studies of milk samples focusing on the health-disease status in dairy cattle are still scarce, which makes it difficult to evaluate the microbial ecophysiology of bovine hindmilk. This study provides an alternative method for genome-centric metagenome studies applied to hindmilk samples with high somatic cell content, which is indispensable to examining host-microbiome interactions in bovine mastitis.
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Affiliation(s)
- Vinícius da Silva Duarte
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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da Silva JD, Melo LDR, Santos SB, Kropinski AM, Xisto MF, Dias RS, da Silva Paes I, Vieira MS, Soares JJF, Porcellato D, da Silva Duarte V, de Paula SO. Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage. Appl Microbiol Biotechnol 2023; 107:7231-7250. [PMID: 37741937 PMCID: PMC10638138 DOI: 10.1007/s00253-023-12743-6] [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: 04/03/2023] [Revised: 04/03/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.
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Affiliation(s)
- Jéssica Duarte da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mariana Fonseca Xisto
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Isabela da Silva Paes
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcella Silva Vieira
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - José Júnior Ferreira Soares
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Vinícius da Silva Duarte
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
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Zhu H, Miao R, Tao X, Wu J, Liu L, Qu J, Liu H, Sun Y, Li L, Qu Y. Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows. Animals (Basel) 2023; 13:1923. [PMID: 37370433 DOI: 10.3390/ani13121923] [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: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d-15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.
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Affiliation(s)
- Huan Zhu
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- College of Science, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Renfang Miao
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Xinxu Tao
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Jianhao Wu
- Bright Farming Co., Ltd., No. 1518, West Jiangchang Road, Shanghai 200436, China
| | - Licheng Liu
- Institute of Animal Husbandry and Veterinary Medicine, Heilongjiang Academy of Agricultural Reclamation, No. 101 Xiangfu Road, Herbin 150038, China
| | - Jiachen Qu
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Hongzhi Liu
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Yanting Sun
- School of Civil Engineering, Xi'an University of Architecture & Technology, No. 99 Yanta Road, Xi'an 710064, China
| | - Lingyan Li
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
| | - Yongli Qu
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, No. 5 Xinyang Road, Daqing 163319, China
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Winther AR, da Silva Duarte V, Porcellato D. Metataxonomic analysis and host proteome response in dairy cows with high and low somatic cell count: a quarter level investigation. Vet Res 2023; 54:32. [PMID: 37016420 PMCID: PMC10074679 DOI: 10.1186/s13567-023-01162-0] [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: 07/13/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
Host response to invasive microbes in the bovine udder has an important role on the animal health and is essential to the dairy industry to ensure production of high-quality milk and reduce the mastitis incidence. To better understand the biology behind these host-microbiome interactions, we investigated the somatic cell proteomes at quarter level for four cows (collected before and after milking) using a shotgun proteomics approach. Simultaneously, we identified the quarter microbiota by amplicon sequencing to detect presence of mastitis pathogens or other commensal taxa. In total, 32 quarter milk samples were analyzed divided in two groups depending on the somatic cell count (SCC). The high SCC group (>100,000 cell/mL) included 10 samples and significant different proteome profiles were detected. Differential abundance analysis uncovers a specific expression pattern in high SCC samples revealing pathways involved in immune responses such as inflammation, activation of the complement system, migration of immune cells, and tight junctions. Interestingly, different proteome profiles were also identified in quarter samples containing one of the two mastitis pathogens, Staphylococcus aureus and Streptococcus uberis, indicating a different response of the host depending on the pathogen. Weighted correlation network analysis identified three modules of co-expressed proteins which were correlated with the SCC in the quarters. These modules contained proteins assigned to different aspects of the immune response, but also amino sugar and nucleotide sugar metabolism, and biosynthesis of amino acids. The results of this study provide deeper insights on how the proteome expression changes at quarter level in naturally infected cows and pinpoint potential interactions and important biological functions during host-microbe interaction.
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Affiliation(s)
- Anja Ruud Winther
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, Ås, Norway.
| | - Vinícius da Silva Duarte
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, Ås, Norway
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