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Perdomo A, Calle A. Assessment of microbial communities in a dairy farm from a food safety perspective. Int J Food Microbiol 2024; 423:110827. [PMID: 39043054 DOI: 10.1016/j.ijfoodmicro.2024.110827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/11/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024]
Abstract
Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.
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Affiliation(s)
- Angela Perdomo
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Alexandra Calle
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA.
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Seethalakshmi PS, Kumaresan TN, Vishnu Prasad Nair RU, Prathiviraj R, Seghal Kiran G, Selvin J. Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples. Arch Microbiol 2024; 206:314. [PMID: 38900289 DOI: 10.1007/s00203-024-04047-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
In the field of metagenomic research, the choice of DNA extraction methods plays a pivotal yet often underestimated role in shaping the reliability and interpretability of microbial community data. This study delves into the impact of five commercially available DNA extraction kits on the analysis of bovine fecal microbiota. Recognizing the importance of accurate DNA extraction in elucidating microbial community dynamics, we systematically assessed DNA yield, quality, and microbial composition across these kits using 16S rRNA gene sequencing. Notably, the FastDNA spin soil kit yielded the highest DNA concentration, while significant variations in quality were observed across kits. Furthermore, differential abundance analysis revealed kit-specific biases that impacted taxa representation. Microbial richness and diversity were significantly influenced by the choice of extraction kit, with QIAamp DNA stool minikit, QIAamp Power Pro, and DNeasy PowerSoil outperforming the Stool DNA Kit. Principal-coordinate analysis revealed distinct clustering based on DNA isolation procedures, particularly highlighting the unique microbial community composition derived from the Stool DNA Kit. This study also addressed practical implications, demonstrating how kit selection influences the concentration of Gram-positive and Gram-negative bacterial taxa in samples. This research highlights the need for consideration of DNA extraction kits in metagenomic studies, offering valuable insights for researchers striving to advance the precision and depth of microbiota analyses in ruminants.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - T N Kumaresan
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | | | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India.
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Fronton F, Villemur R, Robert D, St-Pierre Y. Divergent bacterial landscapes: unraveling geographically driven microbiomes in Atlantic cod. Sci Rep 2024; 14:6088. [PMID: 38480867 PMCID: PMC10938007 DOI: 10.1038/s41598-024-56616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Establishing microbiome signatures is now recognized as a critical step toward identifying genetic and environmental factors shaping animal-associated microbiomes and informing the health status of a given host. In the present work, we prospectively collected 63 blood samples of the Atlantic cod population of the Southern Gulf of Saint Lawrence (GSL) and characterized their 16S rRNA circulating microbiome signature. Our results revealed that the blood microbiome signature was dominated at the phylum level by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria, a typical signature for fish populations inhabiting the GSL and other marine ecosystems. At the genus level, however, we identified two distinct cod groups. While the microbiome signature of the first group was dominated by Pseudoalteromonas, a genus we previously found in the microbiome signature of Greenland and Atlantic halibut populations of the GSL, the second group had a microbiome signature dominated by Nitrobacter and Sediminibacterium (approximately 75% of the circulating microbiome). Cods harboring a Nitrobacter/Sediminibacterium-rich microbiome signature were localized in the most southern part of the GSL, just along the northern coast of Cape Breton Island. Atlantic cod microbiome signatures did not correlate with the weight, length, relative condition, depth, temperature, sex, and salinity, as previously observed in the halibut populations. Our study provides, for the first time, a unique snapshot of the circulating microbiome signature of Atlantic cod populations and the potential existence of dysbiotic signatures associated with the geographical distribution of the population, probably linked with the presence of nitrite in the environment.
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Affiliation(s)
- Fanny Fronton
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Richard Villemur
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Dominique Robert
- Institut des Sciences de la Mer, Université du Québec à Rimouski, 310, allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Yves St-Pierre
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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Ma X, Wang W, Cai L, Xiao M, He F, Liu Z, Chen D, Wang Y, Shen L, Gu Y. Analysis of the microbial diversity in takin ( Budorcas taxicolor) feces. Front Microbiol 2023; 14:1303085. [PMID: 38188576 PMCID: PMC10768053 DOI: 10.3389/fmicb.2023.1303085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The intestinal tract of animals is a complex and dynamic microecosystem that is inextricably linked to the health of the host organism. Takin (Budorcas taxicolor) is a threatened species, and its gut microbiome is poorly understood. Therefore, this study aimed to analyze the microbial community structure and potential pathogens of takin. Methods Takin fecal samples were collected from five sites in a nature reserve to ensure the uniformity of sample collection, determine the effects of different geographical locations on gut microbes, and analyze the differences in microbial communities between sites. Subsequently, high-throughput 16S rDNA gene sequencing was performed to analyze the microbial diversity and potential pathogens in the gut; the findings were verified by isolating and culturing bacteria and metagenomic sequencing. Results and discussion The takin gut microflora consisted mainly of four phyla: Firmicutes (69.72%), Bacteroidota (13.55%), Proteobacteria (9.02%), and Verrucomicrobiota (3.77%), representing 96.07% of all microorganisms. The main genera were UCG-005 (20.25%), UCG-010_unclassified (12.35%), Firmicus_unclassified (4.03%), and Rumino coccsea_unclassified (3.49%), while the main species were assigned to Bacteria_unclassified. Potential pathogens were also detected, which could be used as a reference for the protection of takin. Pseudomonas presented the highest abundance at Shuichiping and may represent the main pathogen responsible for the death of takin at the site. This study provides an important reference for investigating the composition of the bacterial community in the intestine of takin.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weichen Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lijun Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Mei Xiao
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Fang He
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Sichuan Provincial Center for Animal Disease Prevention and Control, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Limin Shen
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China
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Zhang J, Luo Z, Li N, Yu Y, Cai M, Zheng L, Zhu F, Huang F, K Tomberlin J, Rehman KU, Yu Z, Zhang J. Cellulose-degrading bacteria improve conversion efficiency in the co-digestion of dairy and chicken manure by black soldier fly larvae. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119156. [PMID: 37837764 DOI: 10.1016/j.jenvman.2023.119156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 10/16/2023]
Abstract
Black soldier fly larvae (BSFL) have potential utility in converting livestock manure into larval biomass as a protein source for livestock feed. However, BSFL have limited ability to convert dairy manure (DM) rich in lignocellulose. Our previous research demonstrated that feeding BSFL with mixtures of 40% dairy manure and 60% chicken manure (DM40) provides a novel strategy for significantly improving their efficiency in converting DM. However, the mechanisms underlying the efficient conversion of DM40 by BSFL are unclear. In this study, we conducted a holistic study on the taxonomic stucture and potential functions of microbiota in the larval gut and manure during the DM and DM40 conversion by BSFL, as well as the effects of BSFL on cellulosic biodegradation and biomass production. Results showed that BSFL can consume cellulose and other nutrients more effectively and harvest more biomass in a shorter conversion cycle in the DM40 system. The larval gut in the DM40 system yielded a higher microbiota complexity. Bacillus and Amphibacillus in the BSFL gut were strongly correlated with the larval cellulose degradation capacity. Furthermore, in vitro screening results for culturable cellulolytic microbes from the larval guts showed that the DM40 system isolated more cellulolytic microbes. A key bacterial strain (DM40L-LB110; Bacillus subtilis) with high cellulase activity from the larval gut of DM40 was validated for potential industrial applications. Therefore, mixing an appropriate proportion of chicken manure into DM increased the abundance of intestinal bacteria (Bacillus and Amphibacillus) producing cellulase and improved the digestion ability (particularly cellulose degradation) of BSFL to cellulose-rich manure through changes in microbial communities composition in intestine. This study reveals the microecological mechanisms underlying the high-efficiency conversion of cellulose-rich manure by BSFL and provide potential applications for the large-scale cellulose-rich wastes conversion by intestinal microbes combined with BSFL.
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Affiliation(s)
- Jia Zhang
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Zhijun Luo
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Nan Li
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yongqiang Yu
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Minmin Cai
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Longyu Zheng
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Fengling Zhu
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Feng Huang
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China.
| | | | - Kashif Ur Rehman
- Department of Microbiology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Ziniu Yu
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Jibin Zhang
- National Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, China
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Floridia V, Russo N, D'Alessandro E, Lopreiato V, Pino A, Amato A, Liotta L, Caggia C, Randazzo CL. Effect of olive cake supplementation on faecal microbiota profile of Holstein and Modicana dairy cattle. Microbiol Res 2023; 277:127510. [PMID: 37801779 DOI: 10.1016/j.micres.2023.127510] [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: 07/12/2023] [Revised: 09/21/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
The present study aimed to investigate the effect of olive cake supplementation on faecal microbiota of Holstein (n = 16) and Modicana (n = 16) dairy cows. Although no difference in richness was detected, within breeds and between the two dietary treatment, the PERMANOVA analysis applied to the beta diversity allowed to discriminate samples according to breeds (p < 0.001) and treatment (p < 0.001). In Holstein cows, the olive cake supplementation led to the increase of Pseudobutyrivibrio and Christensenellaceae_R7-group genera (p < 0.05) recognized as health-promoting or associated with feed efficiency. Differently, no difference was detected between control and treated groups for Modicana suggesting a high adaptive capacity to diet changes. In addition, the higher prevalence of Firmicutes phyla in the Modicana microbiota reflected its better capacity to digest the fibrous sources. Our study supports the suitability of olive cake as a feed supplement for cows and could help validating a sustainable livestock system in the Mediterranean area, characterized by a relevant oil production and by a native breeds reared with extensive systems.
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Affiliation(s)
- Viviana Floridia
- Department of Veterinary Sciences, University of Messina, Polo Universitario Annunziata, 98168 Messina, Italy
| | - Nunziatina Russo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy; ProBioEtna srl, Spin-off of University of Catania, Via S. Sofia, 100, 95123 Catania, Italy
| | - Enrico D'Alessandro
- Department of Veterinary Sciences, University of Messina, Polo Universitario Annunziata, 98168 Messina, Italy
| | - Vincenzo Lopreiato
- Department of Veterinary Sciences, University of Messina, Polo Universitario Annunziata, 98168 Messina, Italy
| | - Alessandra Pino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy; ProBioEtna srl, Spin-off of University of Catania, Via S. Sofia, 100, 95123 Catania, Italy.
| | - Annalisa Amato
- Department of Veterinary Sciences, University of Messina, Polo Universitario Annunziata, 98168 Messina, Italy
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, Polo Universitario Annunziata, 98168 Messina, Italy
| | - Cinzia Caggia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy; ProBioEtna srl, Spin-off of University of Catania, Via S. Sofia, 100, 95123 Catania, Italy
| | - Cinzia Lucia Randazzo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Santa Sofia 100, 95123 Catania, Italy; ProBioEtna srl, Spin-off of University of Catania, Via S. Sofia, 100, 95123 Catania, Italy
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Zhang X, Miao Q, Tang B, Mijakovic I, Ji XJ, Qu L, Wei Y. Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:182. [PMID: 38012750 PMCID: PMC10683242 DOI: 10.1186/s13068-023-02435-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.
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Affiliation(s)
- Xiaoling Zhang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qin Miao
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Bingling Tang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lingbo Qu
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Dimba NR, Mzimela N, Mosili P, Ngubane PS, Khathi A. Investigating the Association Between Diet-Induced "Leaky Gut" and the Development of Prediabetes. Exp Clin Endocrinol Diabetes 2023; 131:569-576. [PMID: 37751850 DOI: 10.1055/a-2181-6664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
INTRODUCTION Chronic consumption of a high-calorie diet compromises the gut microbiota and the integrity of the intestinal wall, which causes translocation of bacterial lipopolysaccharides (LPS) into the blood. This elicits the secretion of pro-inflammatory cytokines, resulting in inflammation. However, how a high-fat high carbohydrate diet affects intestinal permeability and its possible role in the development of prediabetes have not been investigated. This study investigated the effects of HFHC diet-induced prediabetes on gut microbiota and intestinal permeability in male Sprague Dawley rats. METHODS The animals were randomly assigned into the non-prediabetic (NPD) and diet-induced prediabetic (PD) groups (n=6) for 20 weeks. Then, the fecal samples were analyzed to measure the gut microbiota level of Firmicutes, Bacteroidetes, and Proteobacteria in both animal groups. Blood glucose, plasma insulin, serum zonulin, plasma LPS, soluble CD14, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), C-reactive protein (CRP), and intestinal fatty-acid binding protein (IFABP) concentrations were measured. RESULTS The PD group had a reduction in the Firmicutes and an increase in Bacteroidetes and Proteobacteria levels compared to those in the NPD group. Blood glucose, insulin concentration, serum zonulin, and plasma sCD14 concentrations in the PD group increased significantly, while plasma LPS concentrations were similar to the NPD group. Concentrations of plasma TNF-α, IL-6, CRP, and IFABP, an intracellular protein expressed in the intestine, increased in PD compared to the NPD group. CONCLUSIONS the study results cumulatively suggest that chronic consumption of the HFHC diet may be associated with the dysregulation of gut microbiota, leading to increased intestinal permeability.
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Affiliation(s)
- Nosipho R Dimba
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Westville, South Africa, 4000
| | - Nhlakanipho Mzimela
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Westville, South Africa, 4000
| | - Palesa Mosili
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Westville, South Africa, 4000
| | - Phikelelani S Ngubane
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Westville, South Africa, 4000
| | - Andile Khathi
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Westville, South Africa, 4000
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Qin Y, Huang W, Yang J, Zhao Y, Zhao M, Xu H, Zhang M. The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang. Foods 2023; 12:3928. [PMID: 37959048 PMCID: PMC10647823 DOI: 10.3390/foods12213928] [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: 09/28/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.
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Affiliation(s)
- Yanan Qin
- Correspondence: ; Tel.: +86-13999236502
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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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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem. Sci Rep 2023; 13:4056. [PMID: 36906688 PMCID: PMC10008532 DOI: 10.1038/s41598-023-30916-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.
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