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Stefanini R, Karekar S, Ale Enriquez F, Ahring B. Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens. Microbiol Spectr 2024:e0318323. [PMID: 38904373 DOI: 10.1128/spectrum.03183-23] [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: 10/26/2023] [Accepted: 04/13/2024] [Indexed: 06/22/2024] Open
Abstract
We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general. IMPORTANCE Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.
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Affiliation(s)
- Renan Stefanini
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Supriya Karekar
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Fuad Ale Enriquez
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| | - Birgitte Ahring
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
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2
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Víquez-R L, Henrich M, Riegel V, Bader M, Wilhelm K, Heurich M, Sommer S. A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts. Anim Microbiome 2024; 6:28. [PMID: 38745212 PMCID: PMC11094858 DOI: 10.1186/s42523-024-00315-6] [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: 07/25/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.
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Affiliation(s)
- Luis Víquez-R
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany.
- Department of Biology, Bucknell University, Lewisburg, PA, USA.
| | - Maik Henrich
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Grafenau, Bayern, Germany
- Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Vanessa Riegel
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Marvin Bader
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany
- Albert-Ludwigs University, Freiburg, Baden-Württemberg, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Marco Heurich
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Grafenau, Bayern, Germany
- Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Baden-Württemberg, Germany
- Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, NO-34, Norway
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Baden-Württemberg, Germany.
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Do TH, Dao TK, Nguyen HD, Truong NH. Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis. INSECTS 2023; 14:832. [PMID: 37999031 PMCID: PMC10671698 DOI: 10.3390/insects14110832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.
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Affiliation(s)
- Thi Huyen Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
| | - Trong Khoa Dao
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
| | - Hong Duong Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
| | - Nam Hai Truong
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
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Choudhury PK, Jena R, Puniya AK, Tomar SK. Isolation and characterization of reductive acetogens from rumen fluid samples of Murrah buffaloes. 3 Biotech 2023; 13:265. [PMID: 37415727 PMCID: PMC10319699 DOI: 10.1007/s13205-023-03688-8] [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: 09/15/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
In the present study, attempts have been made to isolate reductive acetogens from the rumen fluid samples of Murrah buffaloes (Bubalus bubalis). Out of 32 rumen samples 51 isolates were isolated, and based on autotrophic growth for production of acetate and presence of formyltetrahydrofolate synthetase gene (FTHFS) 12 isolates were confirmed as reductive acetogens. Microscopic observations showed that ten isolates as Gram-positive rods (ACB28, ACB29, ACB66, ACB73, ACB81, ACB91, ACB133, ACB229, ACB52, ACB95) and two isolates as Gram-positive cocci (ACB19, ACB89). All isolates tested negative for catalase, oxidase, and gelatin liquefaction, whereas the production of H2S was detected for two (ACB52 and ACB95) of the above isolates. All these isolates showed autotrophic growth from H2 and CO2, and heterotrophic growth with different fermentable sugars, viz., d-glucose, D-fructose, and D-trehalose but failed to grow on salicin, raffinose, and l-rhamnose. Out of the isolates, two showed amylase activity (ACB28 and ACB95), five showed CMCase activity (ACB19, ACB28, ACB29, ACB73 and ACB91), three showed pectinase activity (ACB29, ACB52 and ACB89), whereas none of the isolates was found positive for avicellase and xylanase activity. Based on 16S rDNA gene sequence analysis, the isolates showed their phylogenetic relationship with maximum similarity up to 99% to different strains of earlier reported known acetogens of clostridia group including Clostridium sp. (6), Eubacterium limosum (1), Ruminococcus sp. (1) and Acetobacterium woodii (1) except one, i.e., Vagococcus fluvialis. The results indicate that reductive acetogens isolated from the rumen fluid samples of Murrah buffalos are both autotrophic and heterotrophic in nature and further investigations are required to exploit and explore their potential as an alternate hydrogen sink.
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Affiliation(s)
- Prasanta Kumar Choudhury
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
- Department of Dairy Technology, School of Agricultural and Bioengineering, Centurion University of Technology and Management, Paralakhemundi, Odisha 761211 India
| | - Rajashree Jena
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
- Department of Dairy Technology, School of Agricultural and Bioengineering, Centurion University of Technology and Management, Paralakhemundi, Odisha 761211 India
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Sudhir Kumar Tomar
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
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Biester A, Marcano-Delgado AN, Drennan CL. Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases. Biochemistry 2022; 61:2797-2805. [PMID: 36137563 PMCID: PMC9782325 DOI: 10.1021/acs.biochem.2c00425] [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] [Indexed: 01/19/2023]
Abstract
Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO2 by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO2 as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO2-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO2, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO2 and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.
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Affiliation(s)
- Alison Biester
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Andrea N. Marcano-Delgado
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Bio-inspired
Solar Energy Program, Canadian Institute
for Advanced Research, Toronto, ON M5G 1M1, Canada,
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6
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Bhatta R, Rahman H. Effect of an anti-methanogenic supplement on enteric methane emission, fermentation, and whole rumen metagenome in sheep. Front Microbiol 2022; 13:1048288. [PMID: 36478863 PMCID: PMC9719938 DOI: 10.3389/fmicb.2022.1048288] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
A study was conducted to investigate the impact of an anti-methanogenic product supplementation on enteric methane emissions, whole rumen metagenome and ruminal fermentation in sheep. Twelve adult male sheep were randomly divided into two groups of six animals each. Animals were fed ad libitum on a total mixed ration either without (CON) or with an anti-methanogenic supplement (Harit Dhara-HD). The anti-methanogenic supplement contained 22.1% tannic acid in a 3: 1 ratio of condensed and hydrolysable tannins. The supplementation of product revealed a significant reduction in daily enteric methane emission (21.9 vs. 17.2 g/d) and methane yield (23.2 vs. 18.2) without affecting the nutrient intake and digestibility. However, the propionate concentration in the HD treatment group was significantly higher than in the CON group. On the contrary, the ammonia nitrogen concentration was lower. The anti-methanogenic supplement significantly decreased the ruminal protozoa in the HD treatment group. Whole rumen metagenome analysis revealed that the core bacterial (Bacteroidetes and Firmicutes) and archaeal communities (Methanobrevibacter and Methanosarcina) were comparable between the CON and HD treatment groups. However, the supplementation of anti-methanogenic product led to a considerable reduction in the abundance of Proteobacteria, whereas the abundance of Lentisphaerae was greater. The supplementation significantly decreased the abundance of Methanocaldococcus, Methanococcoides, Methanocella, and Methanoregula methanogens. A total of 36 KO related to methanogenesis were identified in this study. The activities of formate dehydrogenase (EC 1.8.98.6) and tetrahydromethanopterin S-methyltransferase (EC 2.1.1.86) were significantly lowered by the anti-methanogenic product supplementation in sheep. In conclusion, the anti-methanogenic supplement has the potential to decrease enteric methane emission (~22%) at the recommended level (5% of DM) of supplementation. The contribution of minor methanogens vulnerable to supplementation to rumen methanogenesis is not known; hence, the culturing of these archaea should be taken on priority for determining the impact on overall rumen methanogenesis.
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Affiliation(s)
- Pradeep Kumar Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | | | - Atul Purushottam Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India,*Correspondence: Atul Purushottam Kolte,
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Habibar Rahman
- International Livestock Research Institute, New Delhi, India
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7
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Thirumalaisamy G, Malik PK, Trivedi S, Kolte AP, Bhatta R. Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep. Front Microbiol 2022; 13:780073. [PMID: 35369442 PMCID: PMC8964344 DOI: 10.3389/fmicb.2022.780073] [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: 09/20/2021] [Accepted: 01/27/2022] [Indexed: 11/30/2022] Open
Abstract
Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23–25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 107 cells/ml), Entodiniomorphs (× 107 cells/ml), and Holotrichs (× 106 cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.
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Affiliation(s)
- Govindasamy Thirumalaisamy
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India.,ICAR-National Dairy Research Institute, Karnal, India
| | - Pradeep Kumar Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Shraddha Trivedi
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | | | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
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Dittoe DK, Olson EG, Ricke SC. IMPACT OF THE GASTROINTESTINAL MICROBIOME AND FERMENTATION METABOLITES ON BROILER PERFORMANCE. Poult Sci 2022; 101:101786. [PMID: 35346496 PMCID: PMC9079343 DOI: 10.1016/j.psj.2022.101786] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dana K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Elena G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA.
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Thomas CM, Taib N, Gribaldo S, Borrel G. Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis. ISME COMMUNICATIONS 2021; 1:47. [PMID: 37938279 PMCID: PMC9723798 DOI: 10.1038/s43705-021-00050-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood-Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.
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Affiliation(s)
- Courtney M Thomas
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Najwa Taib
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Guillaume Borrel
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.
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10
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Xie X, Wang Y, Wei Z, Zhang Y, Zhang C, Zhang S, Yang H, Zhang X, Zhao Y. Continuous insulation strategy of organic waste composting in cold region: Based on cold-adapted consortium. BIORESOURCE TECHNOLOGY 2021; 335:125257. [PMID: 33991879 DOI: 10.1016/j.biortech.2021.125257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Compost is a self-heating process for organic waste. Microbes are the main executors in composting process. However, due to low temperature in winter and low efficiency of composting, a lot of heat is lost in composting. In this study, taking-out and feed-batch composting method (TFC) can supplement nutrition and improve composting microenvironment. Compared with NC, the amount of carbohydrates, protein and fat decomposed by TFC increase by 56.8%, 237% and 122%, respectively, in the composting start-up period (0-100 h). Structure and function of microbial community have changed due to stimulation of cold-adapted consortium. In addition, this study shows that core bacteria stimulate cooperation among different bacteria in the organic components metabolism networks. Finally, based on the important role of cold-adapted consortium, the sustainable heating strategy of composting system is put forward, which converts organic wastes into released heat for daily heating and hot water preparation, leading role of cold-adapted consortium.
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Affiliation(s)
- Xinyu Xie
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yihan Wang
- Department of Chemistry, Tianjin Normal University, Tianjin 300387, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yutong Zhang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, China
| | - Chuang Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shubo Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Yang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xu Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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