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Goldman SL, Sanders JG, Sprockett DD, Landers A, Yan W, Moeller AH. Hackflex library preparation enables low-cost metagenomic profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590092. [PMID: 38712258 PMCID: PMC11071439 DOI: 10.1101/2024.04.23.590092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
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Affiliation(s)
- Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Abigail Landers
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
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Eiamsam-Ang T, Tadee P, Buddhasiri S, Chuammitri P, Kittiwan N, Pascoe B, Patchanee P. Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes. J Med Microbiol 2024; 73. [PMID: 38230911 DOI: 10.1099/jmm.0.001787] [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] [Indexed: 01/18/2024] Open
Abstract
Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.
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Affiliation(s)
- Thanaporn Eiamsam-Ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Songphon Buddhasiri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Phongsakorn Chuammitri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nattinee Kittiwan
- Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang, Thailand
| | - Ben Pascoe
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Ineos Oxford Istitute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Prapas Patchanee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
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St-Pierre B, Perez Palencia JY, Samuel RS. Impact of Early Weaning on Development of the Swine Gut Microbiome. Microorganisms 2023; 11:1753. [PMID: 37512925 PMCID: PMC10385335 DOI: 10.3390/microorganisms11071753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Jorge Yair Perez Palencia
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Ryan S Samuel
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
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Tanpong S, Wongtangtintharn S, Cherdthong A, Prachumchai R, Tengjaroenkul B, Chanjula P, Suntara C, Wachirapakorn C. Recycling of Citric Acid Waste for Potential Use as Animal Feed through Fermentation with Lactic Acid Bacteria and a Mixture of Fibrolytic Enzymes. Animals (Basel) 2022; 12:ani12213049. [PMID: 36359173 PMCID: PMC9658312 DOI: 10.3390/ani12213049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Once improperly managed, the citric acid production industry generates waste, which contributes to pollution and other environmental issues. We proposed that, with sufficient quality improvement, citric acid by-product (CAP) might be used for animal feed, thereby reducing the environmental impact. The aim of the present study was to ferment citric acid by-product (CAP) by inoculation with lactic acid bacteria (LAB) and a fibrolytic enzyme mixture for quality improvement and crude fiber reduction in the waste products. LAB inoculants were L. casei TH14, and the additive enzyme used was a fibrolytic enzyme mixture (glucanase, pectinase, and carboxymethylcellulase) of a small-scale fermentation method. The seven treatments employed in this study were as follows: (1) control (untreated), (2) CAP-inoculated L. casei TH14 at 0.01% DM, (3) CAP-inoculated L. casei TH14 at 0.05% DM, (4) CAP-inoculated enzymes at 0.01% DM, (5) CAP-inoculated enzymes at 0.05% DM, (6) CAP-inoculated L. casei TH14 at 0.01% DM with enzymes at 0.01% DM, and (7) CAP-inoculated L. casei TH14 at 0.05% DM with enzymes at 0.05% DM. The samples were taken on days 1, 7, 14, 21, and 28 of ensiling, both before and after. Four replications were used. The results of the chemical composition of the CAP before and after ensilage inoculated with L. casei TH14 did not show any differences in crude protein, ether extract, ash, or gross energy, but the enzymes significantly (p < 0.05) decreased crude fiber and increased nitrogen-free extract. The combination was especially effective at improving the characteristics of CAP, with a reduction in crude fiber from 21.98% to 22.69%, of neutral detergent fiber (NDF) from 16.01% to 17.54%, and of acid detergent fiber (ADF) from 13.75% to 16.19%. Furthermore, the combination of L. casei TH14 and the enzyme increased crude protein from 1.75% to 2.24% at 28 days of ensiling. Therefore, CAP-inoculated L. casei TH14 did not change in chemical composition, while crude fiber, NDF, and ADF decreased when CAP was inoculated with enzyme. The combination of L. casei TH14 and the enzyme is more effective at improving chemical composition and reducing crude fiber and enhancing carbohydrate breakdown in the CAP. Finally, by enhancing the CAP’s quality, it may be possible to use it in animal feed and minimize its impact on the environment.
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Affiliation(s)
- Sirisak Tanpong
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sawitree Wongtangtintharn
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Anusorn Cherdthong
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Bundit Tengjaroenkul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pin Chanjula
- Animal Production Innovation and Management Division, Faculty of Natural Resources, Hat Yai Campus, Prince of Songkla University, Songkhla 90110, Thailand
| | - Chanon Suntara
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chalong Wachirapakorn
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
- Correspondence: ; Tel.: +66-43202362
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Osei EK, Mahony J, Kenny JG. From Farm to Fork: Streptococcus suis as a Model for the Development of Novel Phage-Based Biocontrol Agents. Viruses 2022; 14:v14091996. [PMID: 36146802 PMCID: PMC9501460 DOI: 10.3390/v14091996] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Bacterial infections of livestock threaten the sustainability of agriculture and public health through production losses and contamination of food products. While prophylactic and therapeutic application of antibiotics has been successful in managing such infections, the evolution and spread of antibiotic-resistant strains along the food chain and in the environment necessitates the development of alternative or adjunct preventive and/or therapeutic strategies. Additionally, the growing consumer preference for “greener” antibiotic-free food products has reinforced the need for novel and safer approaches to controlling bacterial infections. The use of bacteriophages (phages), which can target and kill bacteria, are increasingly considered as a suitable measure to reduce bacterial infections and contamination in the food industry. This review primarily elaborates on the recent veterinary applications of phages and discusses their merits and limitations. Furthermore, using Streptococcus suis as a model, we describe the prevalence of prophages and the anti-viral defence arsenal in the genome of the pathogen as a means to define the genetic building blocks that are available for the (synthetic) development of phage-based treatments. The data and approach described herein may provide a framework for the development of therapeutics against an array of bacterial pathogens.
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Affiliation(s)
- Emmanuel Kuffour Osei
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- Food Bioscience, Teagasc Food Research Centre Moorepark, Fermoy, P61 C996 Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- Correspondence: (J.M.); (J.G.K.); Tel.: +353-21-490-2730 (J.M.); +353-25-42283 (J.G.K.)
| | - John G. Kenny
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- Food Bioscience, Teagasc Food Research Centre Moorepark, Fermoy, P61 C996 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence: (J.M.); (J.G.K.); Tel.: +353-21-490-2730 (J.M.); +353-25-42283 (J.G.K.)
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Gaio D, DeMaere MZ, Anantanawat K, Eamens GJ, Falconer L, Chapman TA, Djordjevic S, Darling AE. Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig. PLoS One 2022; 17:e0270372. [PMID: 35749534 PMCID: PMC9232140 DOI: 10.1371/journal.pone.0270372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.
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Affiliation(s)
- Daniela Gaio
- iThree Institute, University of Technology Sydney, Ultimo, Australia
- * E-mail:
| | | | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Graeme J. Eamens
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Linda Falconer
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Steven Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- iThree Institute, University of Technology Sydney, Ultimo, Australia
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