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Lu H, Chen S, Li F, Zhang G, Geng J, Zhang M, Huang X, Wang Y. Comparative Study of Bacterial Microbiota Differences in the Rumen and Feces of Xinjiang Brown and Holstein Cattle. Animals (Basel) 2024; 14:1748. [PMID: 38929367 PMCID: PMC11200985 DOI: 10.3390/ani14121748] [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: 04/21/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Xinjiang Brown cattle are a unique and widely distributed breed of dual-purpose cattle in the Xinjiang area of China, whose milk production performance differs from Holstein cattle. It has been known that variations in bacterial species of the gastrointestinal tract influence milk protein, fat, and lactose synthesis. However, the microbiota differences between Xinjiang Brown and Holstein cattle are less known. This study aims to compare the bacterial community composition of the rumen and feces of these two cattle breeds under the same dietary and management conditions. The 16s rRNA sequencing data and milk production of 18 Xinjiang Brown cows and 20 Holstein cows on the same farm were obtained for analysis. The results confirmed differences in milk production between Xinjiang Brown and Holstein cattle. Microbiota with different relative abundance between these two cattle breeds were identified, and their biological functions might be related to milk synthesis. This study increases the understanding of the differences in microbiota between Xinjiang Brown and Holstein cattle and might provide helpful information for microbiota composition optimization of these dairy cattle.
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Affiliation(s)
- Haibo Lu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.L.); (G.Z.)
| | - Shaokan Chen
- Beijing Sunlon Livestock Development Company Limited, Beijing 100029, China;
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (F.L.); (M.Z.)
| | - Fengjie Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (F.L.); (M.Z.)
| | - Guoxing Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.L.); (G.Z.)
| | - Juan Geng
- Xinjiang Uygur Autonomous Region Animal Husbandry Station, Urumqi 830000, China;
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (F.L.); (M.Z.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (F.L.); (M.Z.)
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.L.); (G.Z.)
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Muturi SM, Muthui LW, Njogu PM, Onguso JM, Wachira FN, Opiyo SO, Pelle R. Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PLoS One 2021; 16:e0244755. [PMID: 33395690 PMCID: PMC7781671 DOI: 10.1371/journal.pone.0244755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.
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Affiliation(s)
- Samuel Mwangangi Muturi
- Department of Biological Sciences, University of Eldoret, Eldoret, Kenya
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucy Wangui Muthui
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Paul Mwangi Njogu
- Institute for Energy and Environmental Technology, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Justus Mong’are Onguso
- Institute for Bioteschnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | | | - Stephen Obol Opiyo
- OARDC, Molecular and Cellular Imaging Center-Columbus, Ohio State University, Columbus, Ohio, United States of America
- The University of Sacread Heart, Gulu, Uganda
| | - Roger Pelle
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Lackner N, Wagner AO, Markt R, Illmer P. pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion. Microorganisms 2020; 8:E286. [PMID: 32093251 PMCID: PMC7074938 DOI: 10.3390/microorganisms8020286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/11/2023] Open
Abstract
pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, 6020 Innsbruck, Austria; (A.O.W.); (R.M.); (P.I.)
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Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges. J Ind Microbiol Biotechnol 2019; 46:1343-1358. [PMID: 31278525 DOI: 10.1007/s10295-019-02211-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023]
Abstract
Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.
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Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor. PLoS One 2018; 13:e0204831. [PMID: 30289885 PMCID: PMC6173382 DOI: 10.1371/journal.pone.0204831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/14/2018] [Indexed: 11/19/2022] Open
Abstract
Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.
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Shrestha S, Fonoll X, Khanal SK, Raskin L. Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives. BIORESOURCE TECHNOLOGY 2017; 245:1245-1257. [PMID: 28941664 DOI: 10.1016/j.biortech.2017.08.089] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 05/23/2023]
Abstract
Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering.
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Affiliation(s)
- Shilva Shrestha
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA; Department of Molecular Biosciences and Bioengineering (MBBE), University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Xavier Fonoll
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering (MBBE), University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA.
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Murali N, Fernandez S, Ahring BK. Fermentation of wet-exploded corn stover for the production of volatile fatty acids. BIORESOURCE TECHNOLOGY 2017; 227:197-204. [PMID: 28038397 DOI: 10.1016/j.biortech.2016.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 05/12/2023]
Abstract
Volatile fatty acids (VFA) have been used as platform molecules for production of biofuels and bioproducts. In the current study, we examine the VFA production from wet-exploded corn stover through anaerobic fermentation using rumen bacteria. The total VFA yield (acetic acid equivalents) was found to increase from 22.8g/L at 2.5% total solids (TS) to 40.8g/L at 5% TS. It was found that the acetic acid concentration increased from 10g/L to 22g/L at 2.5% and 5% TS, respectively. An increased propionic acid production was seen between day 10 and 20 at 5% TS. Valeric acid (4g/L) was produced at 5% TS and not at 2.5% TS. Composition analysis showed that 50% of the carbohydrates were converted to VFA at 5% TS and 33% at 2.5% TS. Our results show that rumen fermentation of lignocellulosic biomass after wet explosion can produce high concentrations of VFA without addition of external enzymes of importance for the process economics of lignocellulosic biorefineries.
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Affiliation(s)
- Nanditha Murali
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, United States
| | - Sebastian Fernandez
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, United States
| | - Birgitte Kiaer Ahring
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, United States.
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De Vrieze J, Regueiro L, Props R, Vilchez-Vargas R, Jáuregui R, Pieper DH, Lema JM, Carballa M. Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:244. [PMID: 27843490 PMCID: PMC5103597 DOI: 10.1186/s13068-016-0652-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/20/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated. RESULTS The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation. CONCLUSIONS This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Leticia Regueiro
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
- AgResearch, Tennent Drive, Palmerston North, 4442 New Zealand
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
| | - Juan M. Lema
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Marta Carballa
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
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Advances in proteomics for production strain analysis. Curr Opin Biotechnol 2015; 35:111-7. [DOI: 10.1016/j.copbio.2015.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 11/22/2022]
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