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Oladele P, Ngo J, Chang T, Johnson TA. Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure. Microbiol Spectr 2024; 12:e0408423. [PMID: 38717193 PMCID: PMC11237419 DOI: 10.1128/spectrum.04084-23] [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: 11/30/2023] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.
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Affiliation(s)
- Paul Oladele
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer Ngo
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Tiffany Chang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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Ding S, Li J, Wang Y, He S, Xie H, Fu H, Feng Y, Shaheen SM, Rinklebe J, Xue L. Manure derived hydrochar reduced phosphorus loss risk via an alteration of phosphorus fractions and diversified microbial community in rice paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170582. [PMID: 38309349 DOI: 10.1016/j.scitotenv.2024.170582] [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: 11/01/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
Phosphorus (P) loss caused by the irrational use of manure organic fertilizer has become a worldwide environmental problem, which has caused a potential threat to water safety and intensified agricultural non-point source pollution. Hydrothermal carbonization is method with a low-energy consumption and high efficiency to deal with environmental problems. Application of pig manure-derived hydrochar (PMH) to soil exhibited potential of sustainable development compared with the pristine pig manure (PM). However, the effects of PMH on the distribution of P among the fractions/forms and the interaction between microorganisms and P forms and its relevance to the potential loss of P in paddy fields has not been clarified. Therefore, in this study, a soil column experiment was conducted using the untreated soil (control), and the PM, PMH1 (PMH derived at 180 °C), and PMH2 (PMH derived at 260 °C) treated soils (at the dose of 0.05 %) and rice was cultivated to investigate the effects of PM and PMH on the P fractions, mobilization, ad potential loss via the induced changes on soil microbial community after a complete growing season of rice. The trend of P utilization was evaluated by P speciation via continuous extraction and 31P NMR. The addition of PMH reduced the proportion of residual P in soil by 23.8-26.3 %, and increased the proportion of HCl-P and orthophosphate by 116.2-158.6 % and 6.1-6.8 % compared to PM. The abundance of gcd gene developed after the application of PMH2, which enhanced the mobile forms of soil P utilization via secreting gluconic acid. The network diagram analysis concluded that the changes in various P forms were mainly related to Proteobacteria, Bacteroides, Firmicutes and Acidobacteria. The results illustrated that PMH mitigate the potential risk of P loss more than PM by altering P fractions and affecting soil microbial community.
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Affiliation(s)
- Shudong Ding
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Li
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yu Wang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shiying He
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Huifang Xie
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Haibin Fu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yanfang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Sabry M Shaheen
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; King Abdulaziz University, Faculty of Meteorology, Environment, and Arid Land Agriculture, Department of Arid Land Agriculture, 21589 Jeddah, Saudi Arabia; University of Kafrelsheikh, Faculty of Agriculture, Department of Soil and Water Sciences, 33516 Kafr El-Sheikh, Egypt
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, National Agricultural Experiment Station for Agricultural Environment, (Liu He), Ministry of Agriculture and Rural Affairs; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Shi C, Xie P, Ding Z, Niu G, Wen T, Gu W, Lu Y, Wang F, Li W, Zeng J, Shen Q, Yuan J. Inhibition of pathogenic microorganisms in solid organic waste via black soldier fly larvae-mediated management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169767. [PMID: 38176562 DOI: 10.1016/j.scitotenv.2023.169767] [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: 10/20/2023] [Revised: 12/03/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
Inadequately managed solid organic waste generation poses a threat to the environment and human health globally. Biotransformation with the black soldier fly larvae (BSFL) is emerging as talent technology for solid waste management. However, there is a lack of understanding of whether BSFL can effectively suppress potential pathogenic microorganisms during management and the underlying mechanisms. In this study, we investigated the temporal variations of microorganisms in two common types of solid waste, i.e., kitchen waste (KW) and pig manure (PM). Natural composting and composting with BSFL under three different pH levels (pH 5, 7, and 9) were established to explore their impact on microbial communities in compost and the gut of BSFL. The results showed that the compost of kitchen waste and pig manure led to an increase in relative abundance of various potentially pathogenic bacteria. Temporal gradient analyses revealed that the most substantial reduction in the relative abundance and diversity of potentially pathogenic microorganisms occurred when the initial pH of both two wastes were adjusted to 7 upon the introduction of BSFL. Through network and pls-pm analysis, it was discovered that the gut microbiota of BSFL occupied an ecological niche in the compost, inhibiting the proliferation of potentially pathogenic microorganisms. This study has revealed the potential of BSFL in reducing public health risks during the solid waste management process, providing robust support for sustainable waste management.
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Affiliation(s)
- Chaohong Shi
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Penghao Xie
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhexu Ding
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guoqing Niu
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Wen
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjie Gu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China.
| | - Yusheng Lu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Fengying Wang
- Guangzhou Outreach Environmental Technologies Co., Ltd., Guangzhou 510640, China
| | - Wanling Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Jianguo Zeng
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
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4
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Zalewska M, Błażejewska A, Czapko A, Popowska M. Pig manure treatment strategies for mitigating the spread of antibiotic resistance. Sci Rep 2023; 13:11999. [PMID: 37491438 PMCID: PMC10368742 DOI: 10.1038/s41598-023-39204-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023] Open
Abstract
Due to the risk of pathogenic antibiotic-resistant bacteria and their antibiotic-resistance genes transfer from livestock feces to the soil and cultivated crops, it is imperative to find effective on-farm manure treatments to minimize that hazardous potential. An introduced worldwide policy of sustainable development, focus on ecological agricultural production, and the circular economy aimed at reducing the use of artificial fertilizers; therefore, such treatment methods should also maximize the fertilization value of animal manure. The two strategies for processing pig manure are proposed in this study-storage and composting. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, and in the resistome, compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harboring antibiotic resistance genes, including those responsible for multi-drug resistance. Overall, the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to crops and the food chain while providing essential fertilizer ingredients.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Czapko
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.
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5
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Osabutey A, Haleem N, Uguz S, Min K, Samuel R, Albert K, Anderson G, Yang X. Growth of Scenedesmus dimorphus in swine wastewater with versus without solid-liquid separation pretreatment. BIORESOURCE TECHNOLOGY 2023; 369:128434. [PMID: 36473585 DOI: 10.1016/j.biortech.2022.128434] [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: 10/25/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Scenedesmus dimorphus was cultivated in raw and pretreated swine wastewater (SW) with 6-L photobioreactors (PBRs) to investigate the effect of solid-liquid separation on algal growth. The same aerated PBRs containing no algae were used as control. Moderate COD and nitrogen removal from the SW was achieved with the algal PBRs. However, compared to the control reactors, they offered no consistent treatment boost. Improved algal growth occurred in the pretreated SW, as measured by maximum algal cell count (3202 ± 275 × 106 versus 2286 ± 589 × 106 cells L-1) and cell size. The enhanced algal growth in the pretreated SW resulted in relatively high nitrogen (5.7 %) and organic matter contents in the solids harvested at the end of cultivation experiments, with ∼25.6 % of nitrogen in the SW retained in the solids and ∼9.1 % absorbed by algae. The pretreatment also resulted in elevated phosphorus removal. This study is anticipated to foster the development of microalgae-based SW treatment processes.
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Affiliation(s)
- Augustina Osabutey
- Department of Agricultural and Biosystems Engineering, South Dakota State University, Brookings, SD 57007, USA
| | - Noor Haleem
- Department of Agricultural and Biosystems Engineering, South Dakota State University, Brookings, SD 57007, USA; Institute of Environmental Sciences and Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Seyit Uguz
- Biosystems Engineering, Faculty of Agriculture, Bursa Uludag University, Gorukle 16240, Bursa, Turkey
| | - Kyungnan Min
- Department of Civil and Environmental Engineering, South Dakota State University, Brookings, SD 57007, USA
| | - Ryan Samuel
- Department of Animal Science, South Dakota State University, Brookings, SD 57007, USA
| | - Karlee Albert
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Gary Anderson
- Department of Agricultural and Biosystems Engineering, South Dakota State University, Brookings, SD 57007, USA
| | - Xufei Yang
- Department of Agricultural and Biosystems Engineering, South Dakota State University, Brookings, SD 57007, USA.
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Begmatov S, Beletsky AV, Gruzdev EV, Mardanov AV, Glukhova LB, Karnachuk OV, Ravin NV. Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility. Microorganisms 2022; 10:2301. [PMID: 36422370 PMCID: PMC9692488 DOI: 10.3390/microorganisms10112301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 08/26/2023] Open
Abstract
The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Eugeny V. Gruzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Lubov B. Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Do TT, Nolan S, Hayes N, O'Flaherty V, Burgess C, Brennan F, Walsh F. Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119271. [PMID: 35398400 DOI: 10.1016/j.envpol.2022.119271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.
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Affiliation(s)
- Thi Thuy Do
- Maynooth University, Biology Department, Ireland
| | - Stephen Nolan
- National University of Ireland Galway, School of Natural Science and Ryan Institute, Galway, Ireland
| | - Nicky Hayes
- Teagasc, Department of Environment, Soils and Landuse, Johnstown Castle, Wexford, Ireland
| | - Vincent O'Flaherty
- National University of Ireland Galway, School of Natural Science and Ryan Institute, Galway, Ireland
| | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Fiona Brennan
- Teagasc, Department of Environment, Soils and Landuse, Johnstown Castle, Wexford, Ireland
| | - Fiona Walsh
- Maynooth University, Biology Department, Ireland.
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Andersen VD, Jensen MS, Munk P, Vigre H. Robustness in quantifying the abundance of antimicrobial resistance genes in pooled faeces samples from batches of slaughter pigs using metagenomics analysis. J Glob Antimicrob Resist 2021; 24:398-402. [PMID: 33626417 DOI: 10.1016/j.jgar.2021.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES With the continued spread of antimicrobial resistance (AMR) in animals, it is important to assess its occurrence throughout a microbiome quantitatively in order to evaluate significantly affecting factors, e.g. antimicrobial usage. Metagenomics methods make it possible to measure the abundance of AMR genes in complex samples such as pooled faeces samples from batches of slaughter pigs. This study was performed to determine the random error in pooled samples from batches of pigs at slaughter and the measurement error from the metagenomics processes. METHODS In four farms, two pooled samples were obtained from a batch of slaughter pigs by two individual samplers, and each pooled sample was thereafter processed twice. Hierarchically clustered heatmaps were applied to evaluate dissimilarities between samples. The coefficient of variation was used to calculate the percentage difference between samples from the same farm. RESULTS Results of the analysis revealed that it was not possible to quantitatively separate the variation arising from sampling and metagenomics processes. They both contributed to the overall measurement error in batches of slaughter pigs. CONCLUSION Sampling of single pigs in 30 randomly selected pig pens within the farms provides a composition representative for frequently occurring AMR genes present within the farms, while rare genes were not dispersed in a similar manner. Aggregating the resistance abundance at gene family or antimicrobial class level will reduce the apparent variation originating from errors in sampling and metagenomics processing.
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Affiliation(s)
- Vibe Dalhoff Andersen
- The National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, Denmark.
| | - Marie Stengaard Jensen
- The National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, Denmark
| | - Patrick Munk
- The National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, Denmark
| | - Håkan Vigre
- The National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, Denmark
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9
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Im S, Mostafa A, Shin SR, Kim DH. Combination of H 2SO 4-acidification and temperature-decrease for eco-friendly storage of pig slurry. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123063. [PMID: 32512282 DOI: 10.1016/j.jhazmat.2020.123063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Owing to the economic benefit and efficiency, H2SO4-acidification is often applied for reducing CH4 emissions during storage of pig slurry (PS). However, it encounters with several problems related with safety and the concomitant H2S emissions. To reduce the required amount of H2SO4, in this study, the storage at low temperature (20-35 °C) was applied to the mild-acidified PS (pH 6.5 and 7.0). 55.1 kg CO2 eq./ton PS of CH4 was emitted from the control (non-acidified at 35 °C), which was reduced to 14.4-40.2 kg CO2 eq./ton PS at 20-30 °C. Temperature-decrease led to the increase of the abundance of methanogens (Methanobrevibacter and Methanolobus) that can grow at low temperature and the drop of specific methanogenic activity value. To achieve 70 % CH4 reduction, 1.6 kg H2SO4/ton PS was needed in PS acidification, which was decreased to 0.5 kg H2SO4/ton PS by decreasing temperature from 35 °C to 25 °C. CH4 production potential of the PS stored at 35 °C-pH 6.5 and 25 °C-pH 7.0 was increased by 21-33 % compared to the control. The GHG reduction of 33.6-41.9 kg CO2 eq./ton PS and the profit of 6.6 USD/ton PS could be attained by applying acidification or combined storage, indicating that the temperature-decrease can be effectively combined with H2SO4-acidification.
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Affiliation(s)
- Seongwon Im
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea
| | - Sang-Ryong Shin
- Process design team, JEON TECH. Co., Ltd., 77 Haenggung-ro, Paldal-gu, Suwon 16261, Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea.
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Jeong Y, Park J, Kim EB. Changes in Gut Microbial Community of Pig Feces in Response to Different Dietary Animal Protein Media. J Microbiol Biotechnol 2020; 30:1321-1334. [PMID: 32522966 PMCID: PMC9728240 DOI: 10.4014/jmb.2003.03021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/07/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.
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Affiliation(s)
- Yujeong Jeong
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jongbin Park
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea,Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea,Corresponding author Phone: +82-33-250-8642 Fax: +82-33-259-5574 E-mail:
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Karlsson E, Johansson AM, Ahlinder J, Lundkvist MJ, Singh NJ, Brodin T, Forsman M, Stenberg P. Airborne microbial biodiversity and seasonality in Northern and Southern Sweden. PeerJ 2020; 8:e8424. [PMID: 32025374 PMCID: PMC6991134 DOI: 10.7717/peerj.8424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/17/2019] [Indexed: 01/04/2023] Open
Abstract
Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air.
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Affiliation(s)
- Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | | | - Jon Ahlinder
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Navinder J Singh
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mats Forsman
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Per Stenberg
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden.,Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden
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