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Yu Z, Yan M, Somasundaram S. Rumen protozoa and viruses: The predators within and their functions-A mini-review. JDS Commun 2024; 5:236-240. [PMID: 38646576 PMCID: PMC11026968 DOI: 10.3168/jdsc.2023-0433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/07/2023] [Indexed: 04/23/2024]
Abstract
The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.
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Affiliation(s)
- Zhongtang Yu
- Department of Animal Sciences, Center of Microbiome Science, The Ohio State University, Columbus, OH 43210
| | - Ming Yan
- Department of Animal Sciences, Center of Microbiome Science, The Ohio State University, Columbus, OH 43210
| | - Sripoorna Somasundaram
- Department of Animal Sciences, Center of Microbiome Science, The Ohio State University, Columbus, OH 43210
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Pratt CJ, Meili CH, Jones AL, Jackson DK, England EE, Wang Y, Hartson S, Rogers J, Elshahed MS, Youssef NH. Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution. Nat Commun 2024; 15:2714. [PMID: 38548766 PMCID: PMC10978972 DOI: 10.1038/s41467-024-47047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.
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Affiliation(s)
- Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Casey H Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Adrienne L Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Darian K Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Emma E England
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Yan Wang
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Steve Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Qi W, Xue MY, Jia MH, Zhang S, Yan Q, Sun HZ. - Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation. Anim Biosci 2024; 37:370-384. [PMID: 38186256 PMCID: PMC10838668 DOI: 10.5713/ab.23.0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 01/09/2024] Open
Abstract
Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.
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Affiliation(s)
- Wenlingli Qi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Yuan Xue
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Hui Jia
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuxian Zhang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Qiongxian Yan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Hui-Zeng Sun
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Belanche A, Palma-Hidalgo JM, Jiménez E, Yáñez-Ruiz DR. Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats. Front Vet Sci 2023; 10:1272835. [PMID: 38179333 PMCID: PMC10764530 DOI: 10.3389/fvets.2023.1272835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction This study explores if promoting a complex rumen microbiota represents an advantage or a handicap in the current dairy production systems in which ruminants are artificially reared in absence of contact with adult animals and fed preserved monophyte forage. Methods In order to promote a different rumen microbial diversity, a total of 36 newborn goat kids were artificially reared, divided in 4 groups and daily inoculated during 10 weeks with autoclaved rumen fluid (AUT), fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate (RFC) diets, or absence of inoculation (CTL). At 6 months of age all animals were shifted to an oats hay diet to determine their ability to digest a low quality forage. Results and discussion Early life inoculation with fresh rumen fluid promoted an increase in the rumen overall microbial diversity which was detected later in life. As a result, at 6 months of age RFF and RFC animals had higher bacterial (+50 OTUs) and methanogens diversity (+4 OTUs) and the presence of a complex rumen protozoal community (+32 OTUs), whereas CTL animals remained protozoa-free. This superior rumen diversity and presence of rumen protozoa had beneficial effects on the energy metabolism allowing a faster adaptation to the forage diet, a higher forage digestion (+21% NDF digestibility) and an energetically favourable shift of the rumen fermentation pattern from acetate to butyrate (+92%) and propionate (+19%) production. These effects were associated with the presence of certain rumen bacterial taxa and a diverse protozoal community. On the contrary, the presence of rumen protozoa (mostly Entodinium) had a negative impact on the N metabolism leading to a higher bacterial protein breakdown in the rumen and lower microbial protein flow to the host based on purine derivatives urinary excretion (-17% to -54%). The inoculation with autoclaved rumen fluid, as source of fermentation products but not viable microbes, had smaller effects than using fresh inoculum. These findings suggest that enhancing rumen microbial diversity represents a desirable attribute when ruminants are fed forages in which the N supply does not represent a limiting factor for the rumen microbiota.
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Affiliation(s)
- Alejandro Belanche
- Estación Experimental del Zaidín (CSIC), Granada, Spain
- Department of Animal Production and Food Sciences, University of Zaragoza, Zaragoza, Spain
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Takahashi K, Kuwahara H, Horikawa Y, Izawa K, Kato D, Inagaki T, Yuki M, Ohkuma M, Hongoh Y. Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade. ISME J 2023; 17:1895-1906. [PMID: 37653056 PMCID: PMC10579323 DOI: 10.1038/s41396-023-01502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.
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Affiliation(s)
- Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Hirokazu Kuwahara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yutaro Horikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kazuki Izawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Daiki Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Tatsuya Inagaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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