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Fei F, Su Z, Liu R, Gao R, Sun C. Efficient biodegradation of poly(butylene adipate-co-terephthalate) in mild temperature by cutinases derived from a marine fungus. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136008. [PMID: 39368353 DOI: 10.1016/j.jhazmat.2024.136008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/12/2024] [Accepted: 09/28/2024] [Indexed: 10/07/2024]
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT) waste gradually accumulates in the environment, posing ecological risks. Enzymatic hydrolysis holds great potential in the end-of-life management of PBAT, but reported enzymes require high reaction temperatures, limiting their practical industrial applications. In this study, we discovered that the marine fungus Alternaria alternata FB1 can efficiently degrade PBAT at 28 °C. Two cutinases designated as AaCut4 and AaCut10, were identified and verified as key enzymes responsible for this degradation process. Notably, the recombinant AaCut10 was able to depolymerize 82.14 % PBAT within 24 h and fully decompose it within 48 h at 37 °C. Through protein engineering, the yield of terephthalic acid monomer was increased to 96.01 %, highlighting its potential for facilitating PBAT upcycling. Furthermore, based on the investigation of the distribution patterns of PBAT hydrolases, novel degradative agents have been identified within unique ecological niches, leading to the establishment of a comprehensive screening repository of PBAT hydrolases. Overall, our study provides new candidates for enzymatic PBAT recycling with low energy consumption and offers insights into the PBAT degradation manner in ecosystems.
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Affiliation(s)
- Fan Fei
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhenjie Su
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | | | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China.
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Hong Q, Wang K, Huang Y, Zhang Z, Jiang Y, Wang S, Wang H. Enhanced methane production from anaerobic digestion of waste activated sludge with weak magnetic field: Insights into performances and mechanisms. BIORESOURCE TECHNOLOGY 2024; 408:131174. [PMID: 39084537 DOI: 10.1016/j.biortech.2024.131174] [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: 05/23/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
The impact of weak magnetic field (WMF) on anaerobic digestion (AD) performance of waste activated sludge (WAS) and underlying mechanism were investigated. Results showed that WMF significantly stimulated the methane yield by 12.9∼25.1% with 15 and 30 mT WMF addition, but high WMF (60 mT) attenuated the positive effect. The WMF enriched the anaerobic microbes, especially the acetoclastic and hydrogenotrophic methanogen. Additionally, the WMF dramatically facilitated the metabolic pathways of key enzymes for methanogenesis, which was validated by the significant increase of absolute abundance of anaerobic functional genes (mcrA). The enzyme activities of ATP and F420 were also significantly promoted by 30 mT WMF, but high WMF (60 mT) resulted in increased activity of lactate dehydrogenase. This study reveals that low WMF can promote AD performance of WAS through enhancing microbial activities especially methanogen, but high WMF leads to the loss of cell membrane integrity and attenuates its positive effect.
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Affiliation(s)
- Qiankun Hong
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; College of Civil Engineering and Architecture, Zhejiang Tongji Vocational College of Science and Technology, Hangzhou 311231, China
| | - Kanming Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yan Huang
- Ecological and Environmental Monitoring Station of Deqing County, Huzhou 313200, China
| | - Zhengyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yulian Jiang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shengnan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hongyu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Ghedini CP, Silva LHP, Moura DC, Brito AF. Supplementing flaxseed meal with sucrose, flaxseed oil, or both: Effects on milk enterolactone, ruminal microbiota profile, production performance, and nutrient utilization in dairy cows. J Dairy Sci 2024; 107:6834-6851. [PMID: 38762110 DOI: 10.3168/jds.2024-24649] [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: 01/05/2024] [Accepted: 04/01/2024] [Indexed: 05/20/2024]
Abstract
Flaxseed is the richest source of secoisolariciresinol diglucoside, which is converted by ruminal microorganisms primarily to the mammalian lignan enterolactone. Our objective was to investigate the effect of diets containing soybean meal or flaxseed meal (FM) supplemented with sucrose, flaxseed oil, or both, on milk enterolactone concentration yield, diversity, and relative abundance of ruminal bacterial taxa, ruminal fermentation profile, production performance, milk fatty acids (FA) yield, and nutrient utilization in dairy cows. Sixteen Holstein cows (8 multiparous [4 ruminally cannulated] and 8 primiparous) averaging (mean ± SD) 134 ± 54.1 DIM and 679 ± 78.9 kg of BW in the beginning of the study were assigned to treatment sequences in a replicated 4 × 4 Latin square design. Each experimental period lasted 25 d, with 18 d for diet adaptation and 7 d for data and sample collection. Diets were formulated to contain a 60:40 forage:concentrate ratio and included the following (DM basis): (1) 8% soybean meal and 23% ground corn (SBM); (2) 15% FM, 10.7% ground corn, and 5% sucrose (FLX+S); (3) 15% FM, 15.4% ground corn, and 3% flaxseed oil (FLX+O); and (4) 15% FM, 10.2% ground corn, 5% sucrose, and 3% flaxseed oil (FLX+SO). Compared with SBM, the concentration and yield of milk enterolactone increased in cows fed the FM diets but did not differ among FLX+S, FLX+O, and FLX+SO. The relative abundances of the phyla Firmicutes, Verrucomicrobiota, and Actinobacteriota, and those of the bacterial genera Lachnospiraceae NK3A20 group, Eubacterium coprostanoligenes group, Anaeromusa-Anaeroarcus, WCHB1-41, and p-251-o5 decreased, whereas Prevotella and NK4A214 group increased when comparing SBM against at least 1 diet containing FM. Furthermore, the relative abundances of Firmicutes and Actinobacteriota and those of Prevotella, Lachnospiraceae NK3A20 group, Eubacterium coprostanoligenes group, Acetitomaculum, Lachnospiraceae unclassified, NK4A214 group, and Anaeromusa-Anaeroarcus changed (increased or decreased) across the FLX+S, FLX+O, and FLX+SO diets. However, all these changes in the relative abundance of the ruminal bacterial taxa were not conclusively associated with the effect of diets on milk enterolactone. Diets did not affect ruminal pH and concentrations of NH3-N and total VFA. Dry matter intake and yields of milk, milk fat, and milk true protein all decreased in cows fed FLX+O or FLX+SO. Yields of milk total odd-chain FA, branched-chain FA, total <16C FA, and total 16C FA decreased with feeding FLX+O and FLX+SO. The apparent total-tract digestibilities of DM and OM were lowest in the FLX+S and FLX+O diets, with CP and ADF digestibilities lowest in cows receiving FLX+S or FLX+O, respectively. Urinary excretion of total N was lowest with feeding SBM. Contrarily, diets did not affect the urinary excretion of total purine derivatives. In brief, despite the effect of diets on the relative abundance of several ruminal microbiota phyla and genera, we were unable to conclusively associate these changes with increased milk enterolactone in FM-containing diets versus SBM.
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Affiliation(s)
- C P Ghedini
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - L H P Silva
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - D C Moura
- Instituto de Ciências Agrárias e Ambientais, Universidade Federal de Mato Grosso-Campus Sinop, Sinop, MT, Brazil 78557-267
| | - A F Brito
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824.
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Li X, Lippens G, Parrou JL, Cioci G, Esque J, Wang Z, Laville E, Potocki-Veronese G, Labourel A. Biochemical characterization of a SusD-like protein involved in β-1,3-glucan utilization by an uncultured cow rumen Bacteroides. mSphere 2024; 9:e0027824. [PMID: 39012103 PMCID: PMC11351036 DOI: 10.1128/msphere.00278-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
In ruminants, the rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides through the coordinated activities of a diverse microbial community. Bacteroidota is a major phylum in this bovine rumen microbiota. They contain several clusters of genes called polysaccharide utilization loci (PULs) that encode proteins working in concert to capture, degrade, and transport polysaccharides. Despite the critical role of SusD-like proteins for efficient substrate transport, they remain largely unexplored. Here, we present the biochemical characterization of a SusD-like protein encoded by a β-glucan utilization locus from an Escherichia coli metagenomic clone previously isolated by functional screening of the bovine rumen microbiome. In this study, we show that clone 41O1 can grow on laminaritriose, cellotriose, and a mixture of cellobiosyl-cellobiose and glucosyl-cellotriose as sole carbon sources. Based on this, we used various in vitro analyses to investigate the binding ability of 41O1_SusD-like towards these oligosaccharides and the corresponding polysaccharides. We observed a clear binding affinity for β-1,6 branched β-1,3-glucans (laminarins, yeast β-glucan) and laminaritriose. Comparison of the AlphaFold2 model of 41O1_SusD-like with its closest structural homologs highlights a similar pattern of substrate recognition. In particular, three tryptophan residues are shown to be crucial for laminarin recognition. In the context of the cow rumen, we discuss the possible substrates targeted by the 41O1_PUL, such as the (1,3;1,4)-β-d-glucans present in cereal grains or the β-1,3- and (1,3;1,6)-β-d-glucans that are components of the cell wall of ruminal yeasts.IMPORTANCEThe rumen microbiota can majorly impact overall animal health, feed efficiency, and release of harmful substances into the environment. This microbiota is involved in the fermentation of organic matter to provide the host with valuable and assimilable nutrients. Bacteroidota efficiently captures, breaks down, and imports complex polysaccharides through the concerted action of proteins encoded by polysaccharide utilization loci (PULs). Within this system, SusD-like protein has proven necessary for the active internalization of the substrate. Nevertheless, the vast majority of SusD-like proteins characterized to date originate from cultured bacteria. With regard to the diversity and importance of uncultured bacteria in the rumen, further studies are required to better understand the role of polysaccharide utilization loci in ruminal polysaccharide degradation. Our detailed characterization of the 41O1_SusD-like therefore contributes to a better understanding of the carbohydrate metabolism of an uncultured Bacteroides from the cow rumen.
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Affiliation(s)
- Xiaoqian Li
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jean-Luc Parrou
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Gianluca Cioci
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Zhi Wang
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Aurore Labourel
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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Wang H, Zhan J, Jiang H, Jia H, Pan Y, Zhong X, Huo J, Zhao S. Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep. Animals (Basel) 2024; 14:2256. [PMID: 39123781 PMCID: PMC11311065 DOI: 10.3390/ani14152256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.
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Affiliation(s)
- Haibo Wang
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinshun Zhan
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haoyun Jiang
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haobin Jia
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Yue Pan
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiaojun Zhong
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Junhong Huo
- Jiangxi Province Key Laboratory of Animal Green and Healthy Breeding, Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (H.W.); (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Bierworth RM, Ribeiro GO, Terry SA, Malmuthuge N, Penner GB, McKinnon JJ, Hucl P, Randhawa H, Beauchemin KA, Stanford K, Schwartzkopf-Genswein K, Yang WZ, Gruninger R, Guan LL, Gibb D, McAllister TA. High deoxynivalenol and ergot alkaloid levels in wheat grain: effects on growth performance, carcass traits, rumen fermentation, and blood parameters of feedlot cattle. Mycotoxin Res 2024; 40:401-417. [PMID: 38698149 PMCID: PMC11258187 DOI: 10.1007/s12550-024-00534-5] [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: 12/11/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 05/05/2024]
Abstract
This study was designed to assess the impacts of a mixture of deoxynivalenol (DON) and ergot alkaloids (EAs) on growth performance, rumen function, blood parameters, and carcass traits of feedlot cattle. Forty steers (450 ± 6.0 kg) were stratified by weight and randomly allocated to 1 of 4 treatments; control-low (CON-L), control-high (CON-H) which contained low or high wheat screenings that lacked mycotoxins at the same level as the mycotoxin-low (MYC-L; 5.0 mg/kg DON, 2.1 mg/kg EA), and mycotoxin-high (MYC-H: 10 mg/kg DON, 4.2 mg/kg EA) diets that included wheat screening with mycotoxins. Steers were housed in individual pens for a 112-day finishing trial. Intake was 24.8% lower (P < 0.001) for MYC steers compared to CON steers. As a result, average daily gains of MYC steers were 42.1% lower (P < 0.001) than CON steers. Gain to feed ratio was also lower (P < 0.001) for MYC steers compared to CON steers. Platelets, alanine aminotransferase, globulins, and blood urea nitrogen were lower (P ≤ 0.008), and lymphocytes, glutathione peroxidase activity (GPx), and interleukin-10 (IL-10) were elevated (P ≤ 0.002) in MYC steers compared to CON steers. Hot carcass weights and backfat thickness were reduced (P < 0.001) in MYC steers, resulting in leaner (P < 0.001) carcasses and higher (P < 0.007) meat yield compared to CON steers. Results suggest that a mixture of DON and EAs negatively impacted health, performance, and carcass traits of feedlot steers, with the majority of this response likely attributable to EAs. However, more research is needed to distinguish the relative contribution of each mycotoxin to the specific responses observed.
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Affiliation(s)
- R M Bierworth
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - G O Ribeiro
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - S A Terry
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - N Malmuthuge
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - G B Penner
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - J J McKinnon
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - P Hucl
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - H Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - K A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - K Stanford
- Department of Biological Sciences, University of Lethbridge, Alberta, T1K 3M4, Canada
| | - K Schwartzkopf-Genswein
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - W Z Yang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - R Gruninger
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada
| | - L L Guan
- Department of Agricultural Food and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - D Gibb
- Gowan's Feed Consulting, Raymond, AB, T0K 2S0, Canada
| | - T A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge Alberta, T1K 4B1, Canada.
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Guo T, Zhang Q, Wang X, Xu X, Wang Y, Wei L, Li N, Liu H, Hu L, Zhao N, Xu S. Targeted and untargeted metabolomics reveals meat quality in grazing yak during different phenology periods on the Qinghai-Tibetan Plateau. Food Chem 2024; 447:138855. [PMID: 38520902 DOI: 10.1016/j.foodchem.2024.138855] [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: 06/09/2023] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/25/2024]
Abstract
Yak meat is more popular among consumers because of its high nutritional value, but little attention has been paid to its meat quality, which is affected by different phenology periods grass. We hypothesized that seasonal variations in grass composition influenced the ruminal bacteria community, and eventually affected the meat quality of yaks. This study aims to investigate the relationship of meat quality in grazing yak as well as the key rumen bacteria using targeted and untargeted metabolomics and 16S rRNA during different phenology periods. The main three altered metabolic pathways in grazing yak, including amino acids biosynthesis, glutathione metabolism, and fatty acids biosynthesis, were found in the grass period (GP) group compared to the regreen period (RP) and hay period (HP) groups. The GP group had higher concentrations of flavor amino acids (FAA), polyunsaturated fatty acids (PUFA), and a lower ratio of n-6/n-3 compared with the RP group. Correlation analysis results showed that Rikenellaceae_RC9_gut_group was positively correlated with fatty acids and lipid metabolites, which might be involved in lipid metabolism. Pediococcus had a positive correlation with biological peptides, which could be involved in the metabolism of bioactive compounds. In conclusion, grass in different phenology periods was associated with modified amino acids and fatty acids composition of yak meat as well as altered regulation of biological pathways, which was correlated with changes in rumen bacterial communities.
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Affiliation(s)
- Tongqing Guo
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xungang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xianli Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Wei
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Linyong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shixiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
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8
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Wu X, Zhang G, Zhang W, Zhou J, Cong H, Yang G, Liu G. Rumen microbiota helps Tibetan sheep obtain energy more efficiently to survive in the extreme environment of the Qinghai-Tibet Plateau. Front Microbiol 2024; 15:1431063. [PMID: 39113833 PMCID: PMC11303141 DOI: 10.3389/fmicb.2024.1431063] [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: 05/11/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction T-sheep and H-sheep exhibit different environmental adaptability and production performance. The rumen microbiome has co-evolved with hosts and plays a vital role in nutrient digestion and energy metabolism. In our previous study, we found that T-sheep have a higher efficiency in energy metabolism than H-sheep, but the rumen microbial community remains unclear. Methods In this study, we determined the rumen bacterial profile and rumen fermentation parameters to reveal the bacterial profiles and predictive functions among breeds and diets with four different energy levels, as well as the correlation between bacterial profiles and rumen fermentation characteristics. Results The results showed that the rumen total volatile fatty acids (VFAs), acetate, butyrate, total branched-chain VFAs, iso-butyrate, and iso-valerate were higher in T-sheep than H-sheep. The alpha diversity of ruminal bacteria is not affected by dietary energy, but it shows a distinction between the sheep breeds. Specifically, T-sheep rumen bacteria exhibit higher alpha diversity than H-sheep. The beta diversity of ruminal bacteria is not influenced by dietary energy or sheep breeds, indicating similar communities of ruminal bacteria between different diets and sheep breeds. The phyla of Bacteroidetes and Firmicutes predominate in the rumen, with a higher relative abundance of Firmicutes observed in T-sheep than H-sheep. The two most abundant genera in the rumen were Prevotella 1 and Rikenellaceae RC9 gut group. Prevotella 1 is the predominant bacterial genus in the rumen of H-sheep, while the Rikenellaceae RC9 gut group dominates in the rumen of T-sheep. Microbial co-occurrence network analysis reveals that variations in rumen fermentation characteristics result from differences in module abundance, with a higher abundance of VFA-producing modules observed in the rumen of T-sheep. Microbial function prediction analysis showed that dietary energy rarely alters the functional composition of rumen bacteria. However, there were differences in the functions of rumen bacteria between sheep breeds, with T-sheep showing a greater emphasis on energy metabolism-related functions, while H-sheep showed a greater emphasis on protein metabolism-related functions. Discussion These findings provide evidence of the special rumen microbial community that helps T-sheep efficiently obtain energy from low-protein and low-energy diets, enabling them to survive in the extreme environment of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xiukun Wu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Jianwei Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Haitao Cong
- Shandong Huakun Rural Revitalization Institute Co., Ltd., Jinan, China
| | - Guo Yang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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9
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Li S, Sun Y, Guo T, Liu W, Tong X, Zhang Z, Sun J, Yang Y, Yang S, Li D, Min L. Sargassum mcclurei Mitigating Methane Emissions and Affecting Rumen Microbial Community in In Vitro Rumen Fermentation. Animals (Basel) 2024; 14:2057. [PMID: 39061518 PMCID: PMC11274217 DOI: 10.3390/ani14142057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/06/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Methane emissions from ruminants significantly contribute to greenhouse gases. This study explores the methane mitigation effect and mechanism of S. mcclurei through in vitro rumen fermentation, aiming to establish its potential as a feed additive. We investigated the effects of freeze-dried and dried S. mcclurei at supplementation levels of 2%, 5%, and 10% of dry matter on nutrient degradation, ruminal fermentation, methane inhibition, and microbial community structure in in vitro rumen fermentation. The freeze-dried S. mcclurei at 2% supplementation significantly reduced CH4 emissions by 18.85% and enhanced crude protein degradability. However, total VFA and acetate concentrations were lower in both treatments compared to the control. The microbial shifts included a decrease in Lachnospiraceae_NK3A20_group and Ruminococcus and an increase in Selenomonas, Succinivibrio, and Saccharofermentans, promoting propionate production. Additionally, a significant reduction in Methanomicrobium was observed, indicating direct methane mitigation. Freeze-dried S. mcclurei at a 2% supplementation level shows potential as an effective methane mitigation strategy with minimal impact on rumen fermentation, supported by detailed insights into microbial community changes.
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Affiliation(s)
- Shuai Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
- Guangdong Provincial Key Laboratory of Animal Nutrition Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
| | - Yi Sun
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Tongjun Guo
- Key Laboratory of Xinjiang feed biotechnology, Feed Research Institute, Xinjiang Academy of Animal Science, Urumqi 830000, China;
| | - Wenyou Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
- College of Life Sciences and Engineering, Foshan University, Foshan 528231, China;
| | - Xiong Tong
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
| | - Zhifei Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
| | - Jiajie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
| | - Yufeng Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Shuli Yang
- College of Life Sciences and Engineering, Foshan University, Foshan 528231, China;
| | - Dagang Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
| | - Li Min
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.L.); (Y.S.); (W.L.); (X.T.); (Z.Z.)
- Key Laboratory of Xinjiang feed biotechnology, Feed Research Institute, Xinjiang Academy of Animal Science, Urumqi 830000, China;
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10
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Yan W, Wang D, Wang Y, Wang C, Chen X, Liu L, Wang Y, Li YY, Kamagata Y, Nobu MK, Zhang T. Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities. MICROBIOME 2024; 12:121. [PMID: 38970122 PMCID: PMC11225162 DOI: 10.1186/s40168-024-01830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. RESULTS In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. CONCLUSION Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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Affiliation(s)
- Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masaru K Nobu
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
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11
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Song X, Li C, Qiu Z, Wang C, Zeng Q. Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes. ENVIRONMENTAL RESEARCH 2024; 252:119012. [PMID: 38704010 DOI: 10.1016/j.envres.2024.119012] [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: 02/23/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.
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Affiliation(s)
- Xiliang Song
- College of Life Sciences, Dezhou University, De'zhou, 253023, China
| | - Changjiang Li
- School of Environment Science & Spatial Informatics, China University of Mining & Technology, Xuzhou, 221116, China
| | - Zhennan Qiu
- College of Life Sciences, Dezhou University, De'zhou, 253023, China
| | - Chenghui Wang
- College of Life Sciences, Dezhou University, De'zhou, 253023, China
| | - Qiangcheng Zeng
- College of Life Sciences, Dezhou University, De'zhou, 253023, China.
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12
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Lu S, Xu Y, Song X, Li J, Jiang J, Qin C, Wu K, Cui K, Liu Y, Liu Q, Shen S, Li Z. Multi-omics reveal the effects and regulatory mechanism of dietary neutral detergent fiber supplementation on carcass characteristics, amino acid profiles, and meat quality of finishing pigs. Food Chem 2024; 445:138765. [PMID: 38367562 DOI: 10.1016/j.foodchem.2024.138765] [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: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
This study aimed to reveal the effects and regulatory mechanism of dietary NDF on the performance of pigs by multi-omics analysis. Results showed that 16 % dietary NDF significantly improved meat quality, increased flavor amino acid content, and reduced backfat thickness and the feed-to-gain ratio. 16S rDNA sequencing showed that 16 % NDF significantly increased the abundance of Akkermansia, Lachnoclostridium, and Ruminococcus. Transcript analysis showed that genes related to muscle development and lipid metabolism were significantly modified. Metabonomic analysis showed that 16 % NDF significantly increased amino and fatty acid related metabolites. Correlation analysis suggested that 16 % NDF treatment may alter the gut microbiota and metabolites, regulate the expression of genes related to lipid and amino metabolism, and ultimately affect the flavor and performance of pigs. This study provides a novel understanding about the effect and regulatory mechanism of NDF supplements on the finishing pigs and a relevant reference for the improvement of diet formulation.
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Affiliation(s)
- Siyu Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China; College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Xinhui Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Jingyi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Jiaqi Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Chaobin Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Kening Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
| | - Yang Liu
- Guangxi Zhuang Autonomous Region Center for Analysis and Test Research, 530022 Nanning, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
| | - Shuibao Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China.
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Guangxi University, 530004 Nanning, China.
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13
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Mies US, Hervé V, Kropp T, Platt K, Sillam-Dussès D, Šobotník J, Brune A. Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates. mBio 2024; 15:e0082624. [PMID: 38742878 PMCID: PMC11257099 DOI: 10.1128/mbio.00826-24] [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: 03/19/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.
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Affiliation(s)
- Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tom Kropp
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology LEEC, UR 4443, University Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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14
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Wang H, Zhan J, Jia H, Jiang H, Pan Y, Zhong X, Zhao S, Huo J. Relationship between Rumen Microbial Differences and Phenotype Traits among Hu Sheep and Crossbred Offspring Sheep. Animals (Basel) 2024; 14:1509. [PMID: 38791726 PMCID: PMC11117386 DOI: 10.3390/ani14101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
This experiment was conducted to investigate the effect of three-way hybrid sheep and Hu sheep on serum indicators, rumen fermentation, rumen enzyme activity, and microorganisms in sheep. Healthy and similar birth weights from three groups (Hu, n = 11; Charolais × Australian White × Hu, CAH, n = 11; Charolais × Dorper × Hu, CDH, n = 11) were selected to be fed by the ewes until 45 days of age. Subsequently, they were weaned intensively and underwent short-term fattening for 3 months along with selected male lambs fed intensively. During this period, they were fed and watered ad libitum. Blood and rumen fluid were collected and analyzed for serum indicators and rumen fluid microorganisms, enzyme activity, and VFA, respectively, at the end of the fattening period. Compared with Hu lamb, the offspring of the three-way hybrid lamb showed significant improvements in body weight, serum lactate dehydrogenase, and creatinine content. However, there was no significant effect on serum immunity and antioxidant indices. In addition, the rumen fluid volatile fatty acid (VFA) molar concentration and microcrystalline cellulose and lipase content were significantly lower in the three-way hybrid lamb compared to Hu lamb, but β-glucosidase, amylase, pepsin, and VFA molar ratio were not significantly affected. Subsequently, 16S rRNA sequencing diversity analysis revealed that three-way hybrid lamb significantly increased rumen microbial ACE and Chao1 indices compared to Hu lamb. Meanwhile, the abundance of Verrucomicrobiota and Synergistota significantly increased at the phylum level. Correlation analysis showed that Prevotella had the highest proportion, while Rikenellaceae_RC9_gut_group correlated most closely with others genus. The microbial communities isovaleric acid molar concentration and proportion were strongly correlated. In addition, there were significant differences in correlations between microbial communities and isobutyric acid, butyric acid and valeric acid content, and their molar proportion, but they were not significantly correlated with digestive enzymes. From the functional enrichment analysis, it was found that hybrid progeny were mainly enriched in the pyruvate metabolism, microbial metabolism in diverse environments, carbon metabolism, and quorum sensing pathways. In contrast, the Hu sheep were primarily enriched in the cysteine and methionine, amino sugar and nucleotide sugar, and biosynthesis of secondary metabolite pathways. These results suggest that hybridization can play a role in regulating organismal metabolism and improve animal production performance by influencing the structure and characteristics of microbial communities.
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Affiliation(s)
- Haibo Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Jinshun Zhan
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haobin Jia
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Haoyun Jiang
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Yue Pan
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiaojun Zhong
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Junhong Huo
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Science, Nanchang 330200, China; (J.Z.); (H.J.); (H.J.); (Y.P.); (X.Z.)
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15
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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Lange MJ, Silva LHP, Zambom MA, Soder KJ, Brito AF. Feeding alfalfa-grass or red clover-grass mixture baleage: Effect on milk yield and composition, ruminal fermentation and microbiota taxa relative abundance, and nutrient utilization in dairy cows. J Dairy Sci 2024; 107:2066-2086. [PMID: 37863298 DOI: 10.3168/jds.2023-23836] [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: 06/04/2023] [Accepted: 10/01/2023] [Indexed: 10/22/2023]
Abstract
Our goal was to investigate the effect of diets containing baleages harvested from alfalfa-grass or red clover-grass mixture on production performance, ruminal fermentation and microbiota taxa relative abundance, milk fatty acid profile, and nutrient utilization in dairy cows. Twenty Jersey cows (18 multiparous and 2 primiparous) averaging (mean ± SD) 148 ± 45.2 days in milk and 483 ± 65.4 kg of body weight in the beginning of the study were used in a randomized complete block design with repeated measures over time. The experiment lasted 9 wk, with a 2 wk covariate period followed by 7 wk of data and sample collection (wk 4 and 7 used in the statistical analyses). Cows were fed diets containing (dry matter basis) 35% of a concentrate mash and the following forage sources: (1) 65% second- and third-cut (32.5% each) alfalfa-grass mixture baleages (ALF) or (2) 65% second- and third-cut (32.5% each) red clover-grass mixture baleages (RC). Diets did not affect dry matter intake, milk yield, and concentrations of milk fat and true protein. In contrast, milk fat yield tended to decrease and energy-corrected milk yield decreased with feeding RC versus ALF. The apparent total-tract digestibilities of dry matter, organic matter, and ash-free neutral detergent fiber, milk proportions of trans-10 18:1, cis-9,cis-12,cis-15 18:3, and total n-3 fatty acids, ruminal molar proportion of acetate, and plasma concentrations of Leu, Phe, and Val all increased in RC versus ALF. Diet × week interactions were found for several parameters, most notably ruminal molar proportions of propionate and butyrate, ruminal NH3-N, milk urea N, plasma urea N, and plasma His concentrations, urinary N excretion, enteric CH4 production, and all energy efficiency variables. Specifically, ruminal NH3-N and plasma urea N concentrations, urinary excretion of N, and CH4 production decreased in cows fed RC in wk 4 but not in wk 7. Milk urea N concentration decreased and that of plasma His increased with feeding RC during wk 4 and 7, although the magnitude of treatments difference varied between the sampling periods. Efficiency of energy utilization calculated as milk energy/metabolizable energy decreased and that of tissue energy/ME increased in RC versus ALF cows in wk 4, suggesting that ME was portioned toward tissue and not milk in the RC diet. Interactions were also observed for the relative abundance of the rumen bacterial phyla Verrucomicrobiota and Fibrobacterota, with cows offered RC showing greater values than those receiving ALF in wk 4 but no differences in wk 7. Several diet × week interactions were detected in the present study implying short-term treatment responses and warranting further investigations.
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Affiliation(s)
- M J Lange
- Universidade Estadual do Oeste do Paraná, Marechal Cândido Rondon, Paraná, Brazil 85960-000
| | - L H P Silva
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham, NH 03824
| | - M A Zambom
- Universidade Estadual do Oeste do Paraná, Marechal Cândido Rondon, Paraná, Brazil 85960-000
| | - K J Soder
- Pasture Systems and Watershed Management Research Unit, USDA-Agricultural Research Service, University Park, PA 16802-3702
| | - A F Brito
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham, NH 03824.
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17
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Chettri D, Verma AK. Statistical optimization of cellulase production from Bacillus sp. YE16 isolated from yak dung of the Sikkim Himalayas for its application in bioethanol production using pretreated sugarcane bagasse. Microbiol Res 2024; 281:127623. [PMID: 38301380 DOI: 10.1016/j.micres.2024.127623] [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: 07/06/2023] [Revised: 11/03/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024]
Abstract
Cellulolytic bacteria were isolated from yak dung samples collected from different habitats of Sikkim, India. Isolate YE16 from the Yumthang Valley sample showed highest enzyme activity of 7.68 U/mL and was identified as Bacillus sp., which has a sequence similarity of 96.15% with B. velezensis. One factor at a time (OFAT) analysis revealed that an acidic pH of 5 with 37 °C temperature was optimum for maximum enzyme production after 36 hrs of incubation (13.88 U/mL), which was further increased after statistical optimization (34.70 U/mL). Media optimization based on response surface methodology predicted that Carboxymethyl cellulose (CMC) and MgSO4 at concentrations of 30 g/L and 0.525 g/L, respectively, at pH 5.5 to show CMCase activity of 30.612 U/mL, which was consistent with the observed value of 30.25 U/mL and confirmed the model. The crude enzyme also efficiently hydrolyzed alkaline pretreated sugarcane bagasse, releasing 7.09 g/L of glucose equivalent with an ethanol production of 3.05 g.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India.
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18
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Liang J, Zhang R, Chang J, Chen L, Nabi M, Zhang H, Zhang G, Zhang P. Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review. Biotechnol Adv 2024; 71:108308. [PMID: 38211664 DOI: 10.1016/j.biotechadv.2024.108308] [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: 09/03/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.
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Affiliation(s)
- Jinsong Liang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Ru Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Mohammad Nabi
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Haibo Zhang
- College of Resources and Environment, Shanxi Agricultural University, Taigu 030801, China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China.
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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Wang C, Fan J, Ma K, Wang H, Li D, Li T, Ma Y. Effects of adding Allium mongolicum Regel powder and yeast cultures to diet on rumen microbial flora of Tibetan sheep ( Ovis aries). Front Vet Sci 2024; 11:1283437. [PMID: 38450026 PMCID: PMC10914970 DOI: 10.3389/fvets.2024.1283437] [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: 08/26/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
The purpose of this experiment was to study the effect of Allium mongolicum Regel powder (AMR) and yeast cultures (YC) on rumen microbial diversity in Tibetan sheep in different Ecological niches. A total of 40 male Tibetan lambs with an initial weight of 18.56 ± 1.49 kg (6 months old) were selected and divided into four groups (10 sheep/pen; n = 10). In the Control Group, each animal was grazed for 8 h per day, in Group I, each animal was supplemented with 200 g of concentrate per day, in Group II, each animal was supplemented with 200 g of concentrate and 10 g of AMR per day, in Group III, each animal was supplemented with 200 g of concentrate and 20 g of YC per day. The experiment lasted 82 days and consisted of a 7-day per-feeding period and a 75-day formal period. The results indicated that at the phylum level, the abundance of Bacteroidota and Verrucomimicrobiota in L-Group II and L-Group III was increased, while the abundance of Proteobacteria was decreased in the LA (Liquid-Associated) groups. The proportion of F/B in S-Group II and S-Group III was increased compared to S-Group I and S-CON in the SA (Soild-Associated) group. At the genus level, the abundance of uncultured_rumen_bacterium and Eubacterium_ruminantium_group in L-Group II and L-Group III was increased. Furthermore, while the abundance of Rikenellaceae_RC9_gut_group was decreased in the LA, the abundance of Prevotella and Eubacterium_ruminantium_group was increased in the S-Group II and S-Group III compared to S-Group I and S-CON. The abundance of probable_genus_10 was the highest in S-Group II in the SA group. After the addition of YC and AMR, there was an increase in rumen microbial abundance, which was found to be beneficial for the stability of rumen flora and had a positive impact on rumen health.
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Affiliation(s)
- Chunhui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Juan Fan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Keyan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Dengpan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
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20
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Astuti PK, Ayoob A, Strausz P, Vakayil B, Kumar SH, Kusza S. Climate change and dairy farming sustainability; a causal loop paradox and its mitigation scenario. Heliyon 2024; 10:e25200. [PMID: 38322857 PMCID: PMC10845714 DOI: 10.1016/j.heliyon.2024.e25200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
It is arguable at this time whether climate change is a cause or effect of the disruption in dairy farming. Climate change drastically affects the productive performance of livestock, including milk and meat production, and this could be attributed to the deviation of energy resources towards adaptive mechanisms. However, livestock farming also contributes substantially to the existing greenhouse gas pool, which is the causal of the climate change. We gathered relevant information from the recent publication and reviewed it to elaborate on sustainable dairy farming management in a changing climatic scenario, and efforts are needed to gather this material to develop methods that could help to overcome the adversities associated with livestock industries. We summarize the intervention points to reverse these adversities, such as application of genetic technology, nutrition intervention, utilization of chemical inhibitors, immunization, and application of metagenomics, which may help to sustain farm animal production in the changing climate scenario.
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Affiliation(s)
- Putri Kusuma Astuti
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
- Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Afsal Ayoob
- Centre for Animal Adaptation to Environment and Climate Change Studies, Kerala Veterinary and Animal Sciences University, Thrissur, 680651, Kerala, India
| | - Péter Strausz
- Department of Management and Organization, Institute of Management, Corvinus University of Budapest, 1093, Budapest, Hungary
| | - Beena Vakayil
- Centre for Animal Adaptation to Environment and Climate Change Studies, Kerala Veterinary and Animal Sciences University, Thrissur, 680651, Kerala, India
| | - S Hari Kumar
- Centre for Animal Adaptation to Environment and Climate Change Studies, Kerala Veterinary and Animal Sciences University, Thrissur, 680651, Kerala, India
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, 4032, Hungary
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21
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Lawther K, Santos FG, Oyama LB, Huws SA. - Invited Review - Chemical signalling within the rumen microbiome. Anim Biosci 2024; 37:337-345. [PMID: 38186253 PMCID: PMC10838665 DOI: 10.5713/ab.23.0374] [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: 09/18/2023] [Revised: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.
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Affiliation(s)
- Katie Lawther
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Fernanda Godoy Santos
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Linda B Oyama
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Sharon A Huws
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
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22
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Tibbs-Cortes BW, Rahic-Seggerman FM, Schmitz-Esser S, Boggiatto PM, Olsen S, Putz EJ. Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus. Front Vet Sci 2024; 11:1334858. [PMID: 38352039 PMCID: PMC10861794 DOI: 10.3389/fvets.2024.1334858] [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: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination. Methods We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period. Results We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health. Discussion This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.
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Affiliation(s)
- Bienvenido W. Tibbs-Cortes
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Faith M. Rahic-Seggerman
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Steven Olsen
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Ellie J. Putz
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
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23
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Huang J, Xu J, Wu R, Wang J, Yang J, Li Y, Wang B, Xiong W, Guo Y. Influence of Cuticular Waxes from Triticale on Rumen Fermentation: A Metabolomic and Microbiome Profiling Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1592-1606. [PMID: 38198510 DOI: 10.1021/acs.jafc.3c07416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Cuticular wax, a critical defense layer for plants, remains a relatively unexplored factor in rumen fermentation. We investigated the impact of cuticular wax on rumen fermentation using triticale as a model. In total, six wax classes were identified, including fatty acids, aldehydes, alkane, primary alcohol, alkyresorcinol, and β-diketone, with low-bloom lines predominated by 46.05% of primary alcohols and high-bloom lines by 35.64% of β-diketone. Low-wax addition (2.5 g/kg DM) increased the gas production by 19.25% (P < 0.05) and total volatile fatty acids by 6.34% (P > 0.05), and enriched key carbohydrate-fermenting rumen microbes like Saccharofermentans, Ruminococcus, and Prevotellaceae, when compared to non-wax groups. Metabolites linked to nucleotide metabolism, purine metabolism, and protein/fat digestion in the rumen showed a positive correlation with low-wax, benefiting rumen microbes. This study highlights the intricate interplay among cuticular wax, rumen microbiota, fermentation, and metabolomics in forage digestion, providing insights into livestock nutrition and forage utilization.
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Affiliation(s)
- Jiahao Huang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Jiawei Xu
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Ruixin Wu
- Dry-Land Farming Institute of Hebei Academy of Agricultural and Forestry Sciences, Hengshui 053000, P. R. China
| | - Jinjing Wang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Jianfeng Yang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Yuan Li
- Dry-Land Farming Institute of Hebei Academy of Agricultural and Forestry Sciences, Hengshui 053000, P. R. China
| | - Bo Wang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Wangdan Xiong
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257091, P. R. China
| | - Yanjun Guo
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, P. R. China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257091, P. R. China
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24
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Bambi M, Galla G, Donati C, Rovero F, Hauffe HC, Barelli C. Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance. Sci Rep 2024; 14:869. [PMID: 38195759 PMCID: PMC10776872 DOI: 10.1038/s41598-023-50126-z] [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: 01/30/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1-V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.
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Affiliation(s)
- Marina Bambi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudia Barelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
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Rout AK, Tripathy PS, Dixit S, Behera DU, Behera B, Das BK, Behera BK. Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India. Antibiotics (Basel) 2023; 12:1735. [PMID: 38136769 PMCID: PMC10740832 DOI: 10.3390/antibiotics12121735] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway;
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Dibyajyoti Uttameswar Behera
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
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Pundee K, Akeprathumchai S, Tripetchkul S, Salaipeth L. Unveiling the microbial dynamics in vermicomposting with coir pith as earthworm substrate. Heliyon 2023; 9:e22945. [PMID: 38144354 PMCID: PMC10746422 DOI: 10.1016/j.heliyon.2023.e22945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
This study explored the impact of incorporating coir pith, a byproduct of the coconut industry, into the vermicomposting substrate of Eudrilus eugeniae earthworms. The groups were compared based on their diets: cow manure only or cow manure mixed with varying amounts of coir pith. The aim was to assess the effects of coir pith on earthworm growth, mortality and the microbial community involved in vermicomposting. Earthworms fed with higher proportions of coir pith (70 % w/w) experienced reduced growth (0.81 g/worm) and increased mortality (24.67 %) after 5 weeks of vermicomposting. These effects were attributed to the high level of total phenolic content in the system. Coir pith required specific bacteria for digestion and detoxification, and excessive intake disrupted the earthworms' digestion, thus hindering nutrient absorption. The study also examined the microbial composition of the vermicast samples and identified variations based on the diet. Bacterial taxa involved in lignocellulose degradation, such as Bacteriodota, Azospirillum, Chitinophagaceae, Marinomonas and Pantoea, exhibited decreased abundances in treatments with coir pith. Conversely, the abundances of potentially harmful bacteria, such as Aeromonas, increased with higher coir pith inclusion levels. This pioneering investigation sheds light on the feasibility of coir pith use in vermicomposting and emphasises the importance of optimising earthworm diets to enhance microbial ecological functions and improve vermicompost quality.
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Affiliation(s)
- Kanokwan Pundee
- College of Multidisciplinary Sciences, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Saengchai Akeprathumchai
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Sudarut Tripetchkul
- Natural Resource Management and Sustainability Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Lakha Salaipeth
- Natural Resource Management and Sustainability Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
- LigniTech-Lignin Technology Research Group, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
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Yang J, Lan X, Zhou T, Zhang Q, Zhang Z, Li P, Qu B. Effects of cold isostatic press pretreatment of rice straw on microstructure and efficiency of anaerobic digestion for methane production. BIORESOURCE TECHNOLOGY 2023; 386:129488. [PMID: 37454956 DOI: 10.1016/j.biortech.2023.129488] [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: 05/20/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
In this study, rice straw was pretreated using by cold isostatic pressure to disrupt its microstructure and improve the performance of anaerobic digestion, and the optimal process parameters were optimized using the response surface methodology. The results showed that cold isostatic pressure pretreatment under optimal conditions (pressure of 400 MPa and holding time of 9 min) was effective in disrupting the structure of rice straw and improving its biodegradability. The cumulative methane production of the cold isostatic pressure pretreatment group increased by 76% compared to the untreated group. In addition, microbial community analysis showed that the relative abundance of Firmicutes, Halobacterota, DMER64 and Methanosaeta was higher in groups pretreated with cold isostatic pressure than in untreated groups. This study demonstrated the potential of pretreatment of rice straw with cold isostatic pressure to increase methane production during anaerobic digestion.
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Affiliation(s)
- Jiancheng Yang
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Xuan Lan
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Tiantian Zhou
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Quanguo Zhang
- Institute of Agricultural Engineering, Huanghe Science and Technology University, Zhengzhou 450006, China; Key Laboratory of New Materials and Facilities for Rural Renewable Energy, MOA of China, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhiyun Zhang
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Pengfei Li
- Heilongjiang Academy of Black Soil Conservation and Utilization, Key Laboratory Combining Farming & Animal Husbandry, Key Laboratory of Straw Energy Utilization, Harbin 150086, China
| | - Bin Qu
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China.
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Li M, Zi X, Lv R, Zhang L, Ou W, Chen S, Hou G, Zhou H. Cassava Foliage Effects on Antioxidant Capacity, Growth, Immunity, and Ruminal Microbial Metabolism in Hainan Black Goats. Microorganisms 2023; 11:2320. [PMID: 37764163 PMCID: PMC10535588 DOI: 10.3390/microorganisms11092320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) foliage is a byproduct of cassava production characterized by high biomass and nutrient content. In this study, we investigated the effects of cassava foliage on antioxidant capacity, growth performance, and immunity status in goats, as well as rumen fermentation and microbial metabolism. Twenty-five Hainan black goats were randomly divided into five groups (n = 5 per group) and accepted five treatments: 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5) of the cassava foliage silage replaced king grass, respectively. The feeding experiment lasted for 70 d (including 10 d adaptation period and 60 d treatment period). Feeding a diet containing 50% cassava foliage resulted in beneficial effects for goat growth and health, as reflected by the higher average daily feed intake (ADFI), average daily gain (ADG) and better feed conversion rate (FCR), as well as by the reduced serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (CRE), and triglycerides (TG). Meanwhile, cassava foliage improved antioxidant activity by increasing the level of glutathion peroxidase (GSH-Px), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) and lowering malondialdehyde (MDA). Moreover, feeding cassava foliage was also beneficial to immunity status by enhancing complement 3 (C3), complement 4 (C4), immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin M (IgM). Furthermore, the addition of dietary cassava foliage also altered rumen fermentation, rumen bacterial community composition, and metabolism. The abundance of Butyrivibrio_2 and Prevotella_1 was elevated, as were the concentrations of beneficial metabolites such as butyric acid; there was a concomitant decline in metabolites that hindered nutrient metabolism and harmed host health. In summary, goats fed a diet containing 50% cassava foliage silage demonstrated a greater abundance of Butyrivibrio_2, which enhanced the production of butyric acid; these changes led to greater antioxidant capacity, growth performance, and immunity in the goats.
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Affiliation(s)
- Mao Li
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - Xuejuan Zi
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Renlong Lv
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - Lidong Zhang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Wenjun Ou
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Songbi Chen
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Guanyu Hou
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - Hanlin Zhou
- Key Laboratory of Ministry of Agriculture and Rural Affairs for Germplasm Resources Conservation and Utilization of Cassava, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Gene Resources and Germplasm Enhancement in Southern China, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
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Kaur H, Kaur G, Gupta T, Mittal D, Ali SA. Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production. BIOLOGY 2023; 12:1200. [PMID: 37759599 PMCID: PMC10525894 DOI: 10.3390/biology12091200] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/16/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023]
Abstract
Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.
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Affiliation(s)
- Harpreet Kaur
- Division of Biochemistry, ICAR-National Dairy Research Institute (ICAR-NDRI), Karnal 132001, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
- Mark Wainwright Analytical Centre, Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW 2052, Australia
- Steno Diabetes Center Copenhagen, DK-2730 Herlev, Denmark
| | - Taruna Gupta
- Division of Biochemistry, ICAR-National Dairy Research Institute (ICAR-NDRI), Karnal 132001, India
| | - Deepti Mittal
- Division of Biochemistry, ICAR-National Dairy Research Institute (ICAR-NDRI), Karnal 132001, India
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute (ICAR-NDRI), Karnal 132001, India
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
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30
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Liang J, Chang J, Zhang R, Fang W, Chen L, Ma W, Zhang Y, Yang W, Li Y, Zhang P, Zhang G. Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression. CHEMOSPHERE 2023; 336:139242. [PMID: 37330070 DOI: 10.1016/j.chemosphere.2023.139242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.
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Affiliation(s)
- Jinsong Liang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Ru Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Wei Fang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Weifang Ma
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yajie Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Wenjing Yang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yuehan Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin, 300130, China.
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31
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Xiong Y, Wang X, Li X, Guo L, Yang F, Ni K. Exploring the rumen microbiota of Hu lambs in response to diet with paper mulberry. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12614-0. [PMID: 37306709 DOI: 10.1007/s00253-023-12614-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023]
Abstract
Paper mulberry (Broussonetia papyrifera), as a new woody forage with high-protein characteristic, is being widely used in ruminant feeding. However, little is known about the comprehensive microbiota picture of whole ruminal niches (liquid, solid, and epithelium) under paper mulberry diet. To gain a better understanding of feeding paper mulberry on the rumen microbiota, the effects of fresh paper mulberry, paper mulberry silage, or a conventional high-protein alfalfa silage on rumen fermentation products and microbiota in rumen niches of Hu lambs were studied. Forty-five Hu lambs were randomly divided into 3 treatments with 15 replicates in each treatment. No significant difference was observed among treatments in the average daily gain (ADG). The fresh paper mulberry treatment had lower (P < 0.05) pH and higher (P < 0.05) total volatile fatty acids (TVFA) compared with silage treatments, but the fermentation parameters did not show significant differences between paper mulberry silage and alfalfa silage treatments. The Shannon index did not show a significant difference (P < 0.05) among treatments except between fresh paper mulberry and alfalfa silage treatment in rumen epithelial niches. Butyrivibrio and Treponema were the predominant genera in the rumen epithelial fraction, while Prevotella and Rikenellaceae_RC9 dominated in both rumen liquid and solid fractions. These results indicated the paper mulberry supplement did not have distinct impact on the microbial diversity and growth performance compared with alfalfa silage, especially for paper mulberry silage, which might help us develop an alternative animal feeding strategy of replacing alfalfa with paper mulberry. KEY POINTS: • Feeding paper mulberry silage did not show significant impact on the growth performance compared with alfalfa silage treatment. • Feeding fresh paper mulberry reduced rumen pH value and increased total volatile fatty acid. • The microbial diversity did not show significant difference among treatments.
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Affiliation(s)
- Yi Xiong
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Linna Guo
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
- College of Animal Science, Guizhou University, Guiyang, 550525, China.
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Ma Z, Zhou J, Liu T, Zheng C. Evaluation of the representative of using rumen fluid samples from lambs fed pelleted TMR for analysis of prokaryotic communities. Front Microbiol 2023; 14:1190253. [PMID: 37283919 PMCID: PMC10240055 DOI: 10.3389/fmicb.2023.1190253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
The pelleted TMR pulverized the grass during processing, which may result in more solid attached microorganisms in the filtered rumen fluid. The objective of this study was evaluating the necessity of distinguishing physical phases of rumen contents for analysis of prokaryotes communities in rumen of lambs fed pelleted TMR, considering the dissimilarity of diversity and community of bacteria and archaea between fluid and mixed rumen contents. The yield of microbial DNA, bacterial diversity, abundances of fibrolytic bacteria of phylum Fibrobacterota and Spirochaetota, as well as genus Ruminococcus, Lachnospiraceae_NK3A20, Fibrobacter, and F082, and abundance of archaeal Methanimicrococcus in rumen fluid were lower than those in mixed phase of rumen contents (p ≤ 0.05). In conclusion, it is necessary to consider rumen content physical phases when studying the prokaryotic community in rumen of lambs fed pelleted TMR.
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Affiliation(s)
- Zhiyuan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Juwang Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Chen Zheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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33
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Wang B, Zhang L, Shi J, Su Y, Wu D, Xie B. Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw. BIORESOURCE TECHNOLOGY 2023; 376:128926. [PMID: 36940870 DOI: 10.1016/j.biortech.2023.128926] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.
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Affiliation(s)
- Binghan Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Liangmao Zhang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Jianhong Shi
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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34
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Xu H, Huang Y, Xiong X, Zhu H, Lin J, Shi J, Tang C, Xu J. Changes in soil Cd contents and microbial communities following Cd-containing straw return. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121753. [PMID: 37127235 DOI: 10.1016/j.envpol.2023.121753] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
Contamination of soil with cadmium (Cd) threatens food safety and human health. In general, crop straws from contaminated soils could accumulate considerable amounts of Cd. The addition of Cd-containing rice straw can have negative effects on soil environment. In this study, straws varying in Cd concentration were added to soil at a rate of 5% (w/w) to investigate the effects of Cd-containing straw on soil Cd dynamics and soil microbial communities. Results showed that large amounts of Cd, especially bioavailable Cd, were released into soil during the decomposition of Cd-containing straws. The addition of straws with 10, 20 and 40 mg kg-1 Cd increased total Cd in soils from 0.31 mg kg-1 to 0.89, 1.39 and 2.09 mg kg-1, respectively, exceeding the screening value of total Cd < 0.4 mg kg-1 for paddy soils of pH 5.5-6.5 according to Chinese Soil Environmental Quality Standards. Moreover, the addition of Cd-containing straw decreased alpha-diversity of bacterial and fungal communities compared to the clean straw. Indeed, changes in soil factors including pH, Eh, dissolved organic C and Cd level jointly reconstructed soil microbial communities. The addition of Cd-containing straw increased the relative abundance of bacterial species Acidobacteria and Proteobacteria but decreased that of Firmicutes. Meanwhile, it increased the relative abundance of fungal species Basidiomycota and Fusarium which were considered Cd-tolerant. This study revealed the potential environmental risk and the variation of microbial communities caused by increasing soil Cd bioavailability after direct application of Cd-containing rice straw to the field.
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Affiliation(s)
- Haojie Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Yu Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Xinquan Xiong
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Hang Zhu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jiahui Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Animal, Plant & Soil Sciences / La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, Vic, 3086, Australia
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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Yang X, Lu S, Feng Y, Cao C, Zhang Y, Cheng S. Characteristics and properties of a polysaccharide isolated from Wolfiporia cocos as potential dietary supplement for IBS. Front Nutr 2023; 10:1119583. [PMID: 37051119 PMCID: PMC10083290 DOI: 10.3389/fnut.2023.1119583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionAs low FODMAP (Fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet therapy is recommended for most of Irritable Bowel Syndrome (IBS) patients, the consequent insufficient of dietary fibers (DFs) intake exert an adverse impact on intestinal health. It is necessary to find suitable DFs for IBS patients.MethodsThis study extracted a water-insoluble polysaccharide from Wolfiporia cocos (WIP) by alkali-extraction and acid-precipitation method. Its molecular weight was detected by high performance gel permeation chromatography (HPGPC) analysis. The structure of WIP was analyzed by Fourier transform infrared (FT-IR) spectrum, Nuclear Magnetic Resonance (NMR) spectra and X-ray diffraction (XRD). The properties related to stability, digestion, viscosity, osmotic activity, adsorption and fermentation were investigated, aimed to explore the feasibility of WIP as a new DF supplement for patients with IBS. In addition, 16S rRNA sequencing analysis was conducted to explore its effects on IBS-related gut microbiota.Results and DiscussionThe results showed that WIP had a single homogeneous composition and the molecular weight was 8.1 × 103 Da. WIP was indicated as a kind of pyranose form with β anomeric configuration and the main chain of WIP was 1,3-β-glucan with amorphous structure. In addition to good thermal stability, WIP also has low bioavailability and can reach the colon mostly without being digested. Moreover, the low viscosity and osmotic activity, the high water- swelling and water/oil-holding capacity, fructose adsorption capacity and poor fermentation performance of WIP demonstrated that it is suitable for IBS patients. It is worth noting that WIP regulates IBS associated gut microbiota effectively, such as the abundance of Lachnospiraceae and Prevotella. These findings provide a theoretical basis for the development of WIP as a dietary supplement for IBS patients with low FODMAP diet therapy.GRAPHICAL ABSTRACT
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Affiliation(s)
- Xuan Yang
- Department of Food Nutrition and Safety/National R&D Center for Chinese Herbal Medicine Processing Technology, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Shun Lu
- Department of Food Nutrition and Safety/National R&D Center for Chinese Herbal Medicine Processing Technology, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Yuhan Feng
- Department of Food Nutrition and Safety/National R&D Center for Chinese Herbal Medicine Processing Technology, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Chongjiang Cao
- Department of Food Nutrition and Safety/National R&D Center for Chinese Herbal Medicine Processing Technology, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Yanliang Zhang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Nanjing Research Center for Infectious Diseases of Integrated Traditional Chinese and Western Medicine, Nanjing, China
| | - Shujie Cheng
- Department of Food Nutrition and Safety/National R&D Center for Chinese Herbal Medicine Processing Technology, School of Engineering, China Pharmaceutical University, Nanjing, China
- Nanjing Research Center for Infectious Diseases of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- *Correspondence: Shujie Cheng,
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Cui X, Wang Z, Fan Q, Chang S, Yan T, Hou F. Ligularia virgaurea improved nutrient digestion, ruminal fermentation, and bacterial composition in Tibetan sheep grazing on the Qinghai–Tibetan Plateau in winter. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA.
- Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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Zhang J, Yang Y, Lei X, Wang Y, Li Y, Li Z, Yao J. Active dry yeast supplementation benefits ruminal fermentation, bacterial community, blood immunoglobulins, and growth performance in young dairy goats, but not for intermittent supplementation. ANIMAL NUTRITION 2023; 13:289-301. [PMID: 37168451 PMCID: PMC10165222 DOI: 10.1016/j.aninu.2023.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/09/2023] [Indexed: 02/19/2023]
Abstract
This study evaluated the effects of active dry yeast (ADY) supplementation and supplementation strategies on ruminal fermentation, bacterial community, blood metabolites, and growth performance in young dairy goats. Sixty young female Guanzhong dairy goats of similar age (4.00 ± 0.50 months) and BW (19.65 ± 0.41 kg) were randomly divided into 3 groups (n = 20): (1) basal diet group (CON); (2) basal diet continuously supplemented with 3.0 g/goat per day commercial ADY (a proprietary strain of Saccharomyces cerevisiae with 5.0 × 109 cfu/g) group (CSY); (3) basal diet with intermittently supplemented ADY group (ISY; 5 d supplementation with ADY at 4.5 g/goat per day following 5 d of no supplementation). The experiment lasted 67 d with the first 7 d as an adaptive period. Rumen fluid and blood samples were collected bi-weekly. Data were analyzed using the MIXED procedure combined with the SLICE option in SAS. Specific orthogonal contrasts of ADY vs. CON and CSY vs. ISY were also analyzed. During the experimental period, ADY supplementation resulted in greater DMI (P = 0.03), ruminal acetate proportion (P < 0.01) and acetylesterase activity (P = 0.01), and blood contents of glucose (P = 0.01) and IgM (P = 0.02) and tended to have greater ADG (P = 0.05) and paunch girth (P = 0.06) than the CON, despite the propionate proportion (P = 0.03) and contents of total protein (P = 0.04) and IgA (P = 0.03) being lower. The lower ruminal NH3-N (P < 0.01) and blood urea nitrogen (P = 0.07) contents indicated greater nitrogen utilization with ADY supplementation. ADY supplementation showed persistent effects after it was stopped because the BW at 12 months of age (P = 0.03) and birth weight of lambs (P = 0.02) were greater than the CON. However, the ISY did not show those benefits and had significantly lower relative abundances of fiber-degrading related bacteria than the CSY. In conclusion, ADY supplementation, especially continuously supplemented, may enhance ADG and ADG:DMI ratio by improving DMI, ruminal cellulolytic bacteria abundance and enzyme activity, nitrogen utilization, and immune status. These findings provide a theoretical basis for the rational application of ADY and have important practical implications for the design of nutritional strategies in growing dairy goats.
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Zhang Z, Huang B, Gao X, Shi X, Wang X, Wang T, Wang Y, Liu G, Wang C. Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning. Front Microbiol 2023; 14:1105330. [PMID: 36778861 PMCID: PMC9915154 DOI: 10.3389/fmicb.2023.1105330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period. Methods A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period. Results In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01). Discussion Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.
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Ravelo AD, Arce-Cordero JA, Lobo RR, Liu T, Jeong KC, Faciola A. Effects of partially replacing dietary corn with sugars in a dual-flow continuous culture system on the ruminal microbiome. Transl Anim Sci 2023; 7:txad011. [PMID: 36815134 PMCID: PMC9940699 DOI: 10.1093/tas/txad011] [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: 10/29/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The objective of this study was to evaluate the effects of feeding sugars as a replacement for starch on the ruminal microbiome using a dual-flow continuous culture system. Four periods of 10 days each were conducted with 8 fermenters in a 4 × 4 replicated Latin square design. Treatments included: 1) control with corn-CON, 2) molasses-MOL, 3) untreated condensed whey permeate-CWP, and 4) CWP treated with a caustic agent-TCWP as a partial substitute for corn. Sugars were defined as the water-soluble carbohydrates (WSC) concentration. Diets were formulated by replacing 4% of the diet DM in the form of starch from corn with the sugars in byproducts. Microbial samples for DNA analysis were collected from the solid and liquid effluent containers at 3, 6, and 9 h after feeding. Bacterial community composition was analyzed with sequencing the V4 region of the 16S rRNA gene using Illumina MiSeq platform. Data were analyzed with R 4.1.3 packages vegan, lmer, and ggplot to determine the effects of treatment on the relative abundance of taxa in the solid and liquid fractions, as well as the correlation of Acetate: Propionate ratio and pH to taxa relative abundance. Treatments did not affect alpha or beta diversity. At the phylum level the relative abundance of Proteobacteria was increased in CON compared to sugars in the solid fraction. In the liquid fraction, Firmicutes had greater relative abundance in sugar treatments while Bacteroidota and Spirochaetota were present in lower relative abundance in CWP. For solid and liquid samples, the family Lachnospiraceae had greater relative abundance in sugar treatments compared to CON. The decreased relative abundance of Christensenellaceae and Rikenellaceae paired with the greater relative abundance of Selenomonadaceae in CWP could help explain greater propionate molar proportion and decreased ruminal pH previously observed for this treatment. The genera Olsenella a lactic acid-producing bacterium, had the greatest relative abundance in MOL. Incorporating TCWP or MOL as a partial replacement for starch was more conservative of fibrolytic bacterial taxa compared to CWP. Additionally, TCWP did not increase bacterial taxa associated with synthesis of lactate as compared to MOL. Overall, replacing starch with sugars is mostly conservative of the ruminal microbiome; however, changes observed coincide with differences observed in acetate and propionate proportions and ruminal pH.
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Affiliation(s)
- Anay D Ravelo
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA,Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Jose A Arce-Cordero
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA,Escuela de Zootecnia, Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Richard R Lobo
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Ting Liu
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA,Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Kwang C Jeong
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA,Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [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: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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Type IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host. Proc Natl Acad Sci U S A 2022; 119:e2215990119. [PMID: 36454763 PMCID: PMC9894109 DOI: 10.1073/pnas.2215990119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Recent characterization of the obligate episymbiont Saccharibacteria (TM7) belonging to the candidate phyla radiation (CPR) has expanded the extent of microbial diversity. However, the episymbiotic lifestyle of TM7 is still underexploited due to the deficiency of cultivated representatives. Here, we describe gene-targeted TM7 cultivation guided by repurposing epicPCR (emulsion, paired isolation, and concatenation PCR) to capture in situ TM7‒host associations. Using this method, we obtained a novel Saccharibacteria isolate TM7i and its host Leucobacter aridicollis J1 from Cicadae Periostracum, the castoff shell of cicada. Genomic analyses and microscopic characterizations revealed that TM7i could bind to J1 through twitching-like motility mediated by type IV pili (T4P). We further showed that the inhibition of T4P extrusion suppressed the motility and host adherence of TM7i, resulting in its reduced growth. However, the inactivation of T4P had little effect on the growth of TM7i that had already adhered to J1, suggesting the essential role of T4P in host recognition by TM7i. By capturing CPR‒host association and elaborating the T4P-dependent episymbiotic association mechanism, our studies shed light on the distinct yet widespread lifestyle of CPR bacteria.
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Biomimicry of ruminant digestion strategies for accelerating lignocellulose bioconversion in anaerobic digestion. Trends Biotechnol 2022; 40:1401-1404. [PMID: 36068120 DOI: 10.1016/j.tibtech.2022.08.002] [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: 03/23/2022] [Revised: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 01/21/2023]
Abstract
Biomimicking ruminant digestion strategies (RDSs) into anaerobic digestion (AD) enables efficient bioconversion of lignocellulosic biomass. Understanding RDSs is essential to translate their features into designing and developing bioprocesses and bioreactors. Here, we discuss insights into recently developed bioinspired bioprocesses, bioreactors, and future AD systems based on RDSs.
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Community-integrated multi-omics facilitates screening and isolation of the organohalide dehalogenation microorganism. Innovation (N Y) 2022; 4:100355. [PMID: 36506298 PMCID: PMC9730224 DOI: 10.1016/j.xinn.2022.100355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A variety of anthropogenic organohalide contaminants generated from industry are released into the environment and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by metagenomic sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavob a cteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 metagenome-assembled genomes were identified, suggesting that the potential for organohalide hydrolytic dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.
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Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep. Animals (Basel) 2022; 12:ani12223221. [PMID: 36428448 PMCID: PMC9686794 DOI: 10.3390/ani12223221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.
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Smith RH, Glendinning L, Walker AW, Watson M. Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome. Anim Microbiome 2022; 4:57. [PMID: 36401288 PMCID: PMC9673341 DOI: 10.1186/s42523-022-00207-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/24/2022] [Indexed: 11/19/2022] Open
Abstract
Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.
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Wang YL, Wang WK, Wu QC, Zhang F, Li WJ, Li SL, Wang W, Cao ZJ, Yang HJ. In Situ Rumen Degradation Characteristics and Bacterial Colonization of Corn Silages Differing in Ferulic and p-Coumaric Acid Contents. Microorganisms 2022; 10:2269. [PMID: 36422339 PMCID: PMC9695934 DOI: 10.3390/microorganisms10112269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 03/05/2024] Open
Abstract
In plant cell wall, ferulic acid (FA) and p-coumaric acid (pCA) are commonly linked with arabinoxylans and lignin through ester and ether bonds. These linkages were deemed to hinder the access of rumen microbes to cell wall polysaccharides. The attachment of rumen microbes to plant cell wall was believed to have profound effects on the rate and the extent of forage digestion in rumen. The objective of this study was to evaluate the effect of bound phenolic acid content and their composition in corn silages on the nutrient degradability, and the composition of the attached bacteria. Following an in situ rumen degradation method, eight representative corn silages with different FA and pCA contents were placed into nylon bags and incubated in the rumens of three matured lactating Holstein cows for 0, 6, 12, 24, 36, 48, and 72 h, respectively. Corn silage digestibility was assessed by in situ degradation methods. As a result, the effective degradability of dry matter, neutral detergent fibre, and acid detergent fibre were negatively related to the ether-linked FA and pCA, and their ratio in corn silages, suggesting that not only the content and but also the composition of phenolic acids significantly affected the degradation characteristics of corn silages. After 24 h rumen fermentation, Firmicutes, Actinobacteria, and Bacteroidota were observed as the dominant phyla in the bacterial communities attached to the corn silages. After 72 h rumen fermentation, the rumen degradation of ester-linked FA was much greater than that of ester-linked pCA. The correlation analysis noted that Erysipelotrichaceae_UCG-002, Olsenella, Ruminococcus_gauvreauii_group, Acetitomaculum, and Bifidobacterium were negatively related to the initial ether-linked FA content while Prevotella was positively related to the ether-linked FA content and the ratio of pCA to FA. In summary, the present results suggested that the content of ether-linked phenolic acids in plant cell walls exhibited a more profound effect on the pattern of microbial colonization than the fibre content.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hong-Jian Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Hua D, Hendriks WH, Xiong B, Pellikaan WF. Starch and Cellulose Degradation in the Rumen and Applications of Metagenomics on Ruminal Microorganisms. Animals (Basel) 2022; 12:3020. [PMID: 36359144 PMCID: PMC9653558 DOI: 10.3390/ani12213020] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Carbohydrates (e.g., starch and cellulose) are the main energy source in the diets of dairy cows. The ruminal digestion of starch and cellulose is achieved by microorganisms and digestive enzymes. In order to improve their digestibility, the microbes and enzymes involved in starch and cellulose degradation should be identified and their role(s) and activity known. As existing and new analytical techniques are continuously being developed, our knowledge of the amylolytic and cellulolytic microbial community in the rumen of dairy cows has been evolving rapidly. Using traditional culture-based methods, the main amylolytic and cellulolytic bacteria, fungi and protozoa in the rumen of dairy cows have been isolated. These culturable microbes have been found to only account for a small fraction of the total population of microorganisms present in the rumen. A more recent application of the culture-independent approach of metagenomics has acquired a more complete genetic structure and functional composition of the rumen microbial community. Metagenomics can be divided into functional metagenomics and sequencing-based computational metagenomics. Both approaches have been applied in determining the microbial composition and function in the rumen. With these approaches, novel microbial species as well as enzymes, especially glycosyl hydrolases, have been discovered. This review summarizes the current state of knowledge regarding the major amylolytic and cellulolytic microorganisms present in the rumen of dairy cows. The ruminal amylases and cellulases are briefly discussed. The application of metagenomics technology in investigating glycosyl hydrolases is provided and the novel enzymes are compared in terms of glycosyl hydrolase families related to amylolytic and cellulolytic activities.
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Affiliation(s)
- Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Wouter H. Hendriks
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wilbert F. Pellikaan
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. MICROBIOME 2022; 10:183. [PMID: 36280858 PMCID: PMC9594917 DOI: 10.1186/s40168-022-01377-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/19/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. RESULTS To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. CONCLUSIONS The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance. Video Abstract.
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Affiliation(s)
- Lauren M Tom
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martina Aulitto
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Naijia Xiao
- Institute of Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Clifford Louime
- College of Natural Sciences, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Javier A Ceja-Navarro
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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