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Methanogen metabolomics

Leticia Abecia, Gonzalo Martínez-Fernandez, Kate Waddams, Antonio Ignacio Martín-García, Eric Pinloche, Christopher J Creevey, Stuart Edward Denman, Charles James Newbold, David R Yáñez-Ruiz
This work aimed to gain insight into the transition from milk to solid feeding at weaning combining genomics and metabolomics on rumen contents from goat kids treated with a methanogenic inhibitor (bromochloromethane, BCM). Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with BCM after giving birth and over 2 months. One kid per doe in both groups was treated with BCM (k+) for 3 months while the other was untreated (k-). Rumen samples were collected from kids at weaning (W) and 1 (W + 1) and 4 (W + 4) months after and from does at weaning and subjected to 16S pyrosequencing and metabolomics analyses combining GC/LC-MS...
2018: Frontiers in Microbiology
Cristina Saro, Ulli M Hohenester, Mickael Bernard, Marie Lagrée, Cécile Martin, Michel Doreau, Hamid Boudra, Milka Popova, Diego P Morgavi
Modulating the assembly of the ruminal microbiota might have practical implications in production. We tested how an early-life dietary intervention in lambs influences the diversity and function of the ruminal microbiota during and after the intervention. Microbiota resilience during a repeated dietary intervention was also tested. The treatment, aiming to mitigate enteric methane emissions, combined garlic essential oil and linseed oil. Fifty-six lambs and their dams were allocated to two groups and treatment (T1) or placebo (C1) was drenched from birth until 10 weeks of life...
2018: Frontiers in Microbiology
Julia Hassa, Irena Maus, Sandra Off, Alfred Pühler, Paul Scherer, Michael Klocke, Andreas Schlüter
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters...
June 2018: Applied Microbiology and Biotechnology
Zhiman Yang, Xiaohui Xu, Meng Dai, Lin Wang, Xiaoshuang Shi, Rongbo Guo
Acetate can be used as an electron donor to stimulate 2,4-dichlorophenoxyacetic acid (2,4-D), which has not been determined under methanogenic condition. This study applied high-throughput sequencing and methanogenic inhibition approaches to investigate the 2,4-D degradation process using the enrichments obtained from paddy soil. Acetate addition significantly promoted 2,4-D degradation, which was 5-fold higher than in the acetate-unsupplemented enrichments in terms of the 2,4-D degradation rate constant. Dechloromonas and Pseudomonas were the dominant 2,4-D degraders...
May 2017: Bioresource Technology
S Riggio, M Torrijos, G Vives, G Esposito, E D van Hullebusch, J P Steyer, R Escudié
In anaerobic leach-bed reactors (LBRs) co-digesting an easily- and a slowly-degradable substrate, the importance of the leachate flush both on extracting volatile fatty acids (VFAs) at the beginning of newly-started batches and on their consumption in mature reactors was tested. Regarding VFA extraction three leachate flush-rate conditions were studied: 0.5, 1 and 2Lkg(-1)TSd(-1). Results showed that increasing the leachate flush-rate during the acidification phase is essential to increase degradation kinetics...
May 2017: Bioresource Technology
Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes...
January 2017: Environmental Microbiology
Gonzalo Martinez-Fernandez, Stuart E Denman, Chunlei Yang, Jane Cheung, Makoto Mitsumori, Christopher S McSweeney
Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix...
2016: Frontiers in Microbiology
Diego P Morgavi, Estelle Rathahao-Paris, Milka Popova, Julien Boccard, Kristian F Nielsen, Hamid Boudra
The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes...
2015: Frontiers in Microbiology
D J Beale, A V Karpe, J D McLeod, S V Gondalia, T H Muster, M Z Othman, E A Palombo, D Joshi
In this study, laboratory scale digesters were operated to simulate potential shocks to the Anaerobic Digestion (AD) process at a 350 ML/day wastewater treatment plant. The shocks included high (42 °C) and low (32 °C) temperature (either side of mesophilic 37 °C) and a 20% loading of fats, oil and grease (FOG; 20% w:v). These variables were explored at two sludge retention times (12 and 20 days) and two organic loading rates (2.0 and 2.5 kgTS/m(3)day OLR). Metagenomic and metabolomic approaches were then used to characterise the impact of operational shocks in regard to temperature and FOG addition, as determined through monitoring of biogas production, the microbial profile and their metabolism...
January 1, 2016: Water Research
Stefan C H J Turk, Wigard P Kloosterman, Dennis K Ninaber, Karin P A M Kolen, Julia Knutova, Erwin Suir, Martin Schürmann, Petronella C Raemakers-Franken, Monika Müller, Stefaan M A de Wildeman, Leonie M Raamsdonk, Ruud van der Pol, Liang Wu, Margarida F Temudo, Rob A M van der Hoeven, Michiel Akeroyd, Roland E van der Stoel, Henk J Noorman, Roel A L Bovenberg, Axel C Trefzer
Nylon-6 is a bulk polymer used for many applications. It consists of the non-natural building block 6-aminocaproic acid, the linear form of caprolactam. Via a retro-synthetic approach, two synthetic pathways were identified for the fermentative production of 6-aminocaproic acid. Both pathways require yet unreported novel biocatalytic steps. We demonstrated proof of these bioconversions by in vitro enzyme assays with a set of selected candidate proteins expressed in Escherichia coli. One of the biosynthetic pathways starts with 2-oxoglutarate and contains bioconversions of the ketoacid elongation pathway known from methanogenic archaea...
January 15, 2016: ACS Synthetic Biology
Krishna M Singh, Amrutlal K Patel, Ravi K Shah, Bhaskar Reddy, Chaitanya G Joshi
Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis...
August 2015: Journal of Applied Genetics
Sheng-Yong Mao, Wen-Jie Huo, Wei-Yun Zhu
Currently, knowledge about the impact of high-grain (HG) feeding on rumen microbiota and metabolome is limited. In this study, a combination of the 454 pyrosequencing strategy and the mass spectrometry-based metabolomics technique was applied to investigate the effects of increased dietary grain (0%, 25% and 50% maize grain) on changes in whole ruminal microbiota and their metabolites using goat as a ruminant model. We observed a significant influence of HG feeding in shaping the ruminal bacterial community structure, diversity and composition, with an overall dominance of bacteria of the phylum Firmicutes along with a low abundance of Bacteriodetes in the HG group...
February 2016: Environmental Microbiology
Daisuke Sasaki, Kengo Sasaki, Yota Tsuge, Masahiko Morita, Akihiko Kondo
Central metabolite profiles from glucose in microbial communities during methanogenic process were compared between a stable methanogenic reactor (MR) and a deteriorated reactor (DR). The concentrations of intracellular metabolites related to the Embden-Meyerhof and pentose phosphate pathways, with the exception of pyruvate, remained high in the MR, showing increased carbon flux in the glycolysis pathway during stable methanogenesis. Extracellular acetate temporarily accumulated in the MR, consistent with higher ATP level in the MR...
November 2014: Bioresource Technology
Yan Fen Cheng, Wei Jin, Sheng Yong Mao, Wei-Yun Zhu
The metabolomic profile of the anaerobic fungus Piromyces sp. F1, isolated from the rumen of goats, and how this is affected by the presence of naturally associated methanogens, was analyzed by nuclear magnetic resonance spectroscopy. The major metabolites in the fungal monoculture were formate, lactate, ethanol, acetate, succinate, sugars/amino acids and α-ketoglutarate, whereas the co-cultures of anaerobic fungi and associated methanogens produced citrate. This is the first report of citrate as a major metabolite of anaerobic fungi...
October 2013: Asian-Australasian Journal of Animal Sciences
Liping Hao, Fan Lü, Qing Wu, Liming Shao, Pinjing He
To precisely control the application of methyl fluoride (CH3F) for analysis of methanogenic pathways, the influence of 0-10% CH3F on bacterial and archaeal communities in a thermophilic methanogenic sludge was investigated. The results suggested that CH3F acts specifically on acetoclastic methanogenesis. The inhibitory effect stabilized at an initial concentration of 3-5%, with around 90% of the total methanogenic activity being suppressed, and a characteristic of hydrogenotrophic pathway in isotope fractionation was demonstrated under this condition...
2014: PloS One
Anne Daebeler, Martina Gansen, Peter Frenzel
The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH(3)F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0...
2013: PloS One
Lovelia L Mamuad, Seon Ho Kim, Sung Sil Lee, Kwang Keun Cho, Che Ok Jeon, Sang-Suk Lee
Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H(2) with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences...
December 2012: Journal of Microbiology / the Microbiological Society of Korea
Elizabeth Lira-Silva, M Geovanni Santiago-Martínez, Viridiana Hernández-Juárez, Rodolfo García-Contreras, Rafael Moreno-Sánchez, Ricardo Jasso-Chávez
Methanosarcina acetivorans was cultured in the presence of CdCl(2) to determine the metal effect on cell growth and biogas production. With methanol as substrate, cell growth and methane synthesis were not altered by cadmium, whereas with acetate, cadmium slightly increased both, growth and methane rate synthesis. In cultures metabolically active, incubations for short-term (minutes) with 10 µM total cadmium increased the methanogenesis rate by 6 and 9 folds in methanol- and acetate-grown cells, respectively...
2012: PloS One
Hyo Jung Lee, Ji Young Jung, Young Kyoon Oh, Sang-Suk Lee, Eugene L Madsen, Che Ok Jeon
Pyrosequencing of 16S rRNA genes (targeting Bacteria and Archaea) and (1)H nuclear magnetic resonance were applied to investigate the rumen microbiota and metabolites of Hanwoo steers in the growth stage (HGS), Hanwoo steers in the late fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG) in the late fattening stage. This was a two-part investigation. We began by comparing metabolites and microbiota of Hanwoo steers at two stages of husbandry. Statistical comparisons of metabolites and microbial communities showed no significant differences between HFS and HGS (differing by a dietary shift at 24 months and age [67 months versus 12 months])...
September 2012: Applied and Environmental Microbiology
Pattanop Kanokratana, Tanaporn Uengwetwanit, Ukrit Rattanachomsri, Benjarat Bunterngsook, Thidarat Nimchua, Sithichoke Tangphatsornruang, Vethachai Plengvidhya, Verawat Champreda, Lily Eurwilaichitr
A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes...
April 2011: Microbial Ecology
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