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Levent G, Božić A, Petrujkić BT, Callaway TR, Poole TL, Crippen TL, Harvey RB, Ochoa-García P, Corral-Luna A, Yeater KM, Anderson RC. Assessment of Potential Anti-Methanogenic and Antimicrobial Activity of Ethyl Nitroacetate, α-Lipoic Acid, Taurine and L-Cysteinesulfinic Acid In Vitro. Microorganisms 2023; 12:34. [PMID: 38257860 PMCID: PMC10819541 DOI: 10.3390/microorganisms12010034] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Livestock producers need new technologies to maintain the optimal health and well-being of their animals while minimizing the risks of propagating and disseminating pathogenic and antimicrobial-resistant bacteria to humans or other animals. Where possible, these interventions should contribute to the efficiency and profitability of animal production to avoid passing costs on to consumers. In this study, we examined the potential of nitroethane, 3-nitro-1-propionate, ethyl nitroacetate, taurine and L-cysteinesulfinic acid to modulate rumen methane production, a digestive inefficiency that results in the loss of up to 12% of the host's dietary energy intake and a major contributor of methane as a greenhouse gas to the atmosphere. The potential for these compounds to inhibit the foodborne pathogens, Escherichia coli O157:H7 and Salmonella Typhimurium DT104, was also tested. The results from the present study revealed that anaerobically grown O157:H7 and DT104 treated with the methanogenic inhibitor, ethyl nitroacetate, at concentrations of 3 and 9 mM had decreased (p < 0.05) mean specific growth rates of O157:H7 (by 22 to 36%) and of DT104 (by 16 to 26%) when compared to controls (0.823 and 0.886 h-1, respectively). The growth rates of O157:H7 and DT104 were decreased (p < 0.05) from controls by 31 to 73% and by 41 to 78% by α-lipoic acid, which we also found to inhibit in vitro rumen methanogenesis up to 66% (p < 0.05). Ethyl nitroacetate was mainly bacteriostatic, whereas 9 mM α-lipoic acid decreased (p < 0.05) maximal optical densities (measured at 600 nm) of O157:H7 and DT104 by 25 and 42% compared to controls (0.448 and 0.451, respectively). In the present study, the other oxidized nitro and organosulfur compounds were neither antimicrobial nor anti-methanogenic.
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Affiliation(s)
- Gizem Levent
- School of Veterinary Medicine, Texas Tech University, Lubbock, TX 79409, USA;
| | - Aleksandar Božić
- Faculty of Agriculture, Department of Animal Science, University of Novi Sad, 21000 Novi Sad, Serbia;
| | - Branko T. Petrujkić
- Department of Nutrition and Botany, Faculty of Veterinary Medicine, University of Belgrade, 110000 Belgrade, Serbia;
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30609, USA;
| | - Toni L. Poole
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Tawni L. Crippen
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Roger B. Harvey
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Pedro Ochoa-García
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31000, Mexico; (P.O.-G.); (A.C.-L.)
| | - Agustin Corral-Luna
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31000, Mexico; (P.O.-G.); (A.C.-L.)
| | - Kathleen M. Yeater
- United States Department of Agriculture/Agricultural Research Service, Office of the Area Director, 104 Ambrose Hill, Williamsburg, VA 20250, USA
| | - Robin C. Anderson
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
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Dahl SA, Seifert J, Camarinha-Silva A, Hernández-Arriaga A, Windisch W, König A. "Get the best out of what comes in" - adaptation of the microbiota of chamois ( Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps. Front Microbiol 2023; 14:1238744. [PMID: 37849922 PMCID: PMC10577445 DOI: 10.3389/fmicb.2023.1238744] [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: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.
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Affiliation(s)
- Sarah-Alica Dahl
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
| | - Jana Seifert
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Angélica Hernández-Arriaga
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Wilhelm Windisch
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas König
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
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Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. SCIENCE ADVANCES 2023; 9:eadg8687. [PMID: 37756392 PMCID: PMC10530074 DOI: 10.1126/sciadv.adg8687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.
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Affiliation(s)
| | - Bo Zhang
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
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4
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Sun Y, Wang L, Han D, Li J, Liu Y, Tan Y, Pan Z, Yang R, Qu P, Wang Z, Bi Y. Curtanaerobium respiraculi gen. nov., sp. nov., a novel anaerobic bacterium isolated from human bronchoalveolar lavage fluid. Int J Syst Evol Microbiol 2023; 73. [PMID: 37184922 DOI: 10.1099/ijsem.0.005864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Two related anaerobic strains, designated as SWB101512T and SWB19611, were isolated from the bronchoalveolar lavage fluid of two lung cancer patients. Cells were Gram-stain-positive, non-motile and non-spore-forming. Growth could be observed at 26-45 °C (optimum, 37 °C), pH 5.0-8.5 (optimum, pH 7.0) and with 0.5-2.0 % (v/w) NaCl (optimum, 1.0%). The 16S rRNA gene sequences of SWB101512T and SWB19611 showed the highest similarities to Denitrobacterium detoxificans DSM 21843T (91.1 and 91.3 %, respectively). The phylogenetic tree based on the 16S rRNA gene sequences and the core genome sequences demonstrated that the two strains clustered together and formed a distinct lineage within the family Eggerthellaceae. The DNA G+C contents of strains SWB101512T and SWB19611 were 62.0 and 61.9 mol%, respectively. The predominant cellular fatty acids of strains SWB101512T and SWB19611 were C16 : 0 DMA (27.8 and 28.8 %, respectively). The respiratory menaquinone in both strains was menaquinone 6 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, two phospholipids, three glycolipids and three unidentified lipids. Based on evidence from phenotypic, chemotaxonomic and genomic analyses, a new genus and species belonging to the family Eggerthellaceae, named Curtanaerobium respiraculi gen. nov., sp. nov. is proposed. The type strain is SWB101512T (=GDMCC 1.2991T=JCM 35330T).
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Affiliation(s)
- Yifan Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Likun Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Dexing Han
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
| | - Jianjie Li
- Department of Thoracic Foncology, Peking University Cancer Hospital, Beijing, 100142, PR China
| | - Yuejiao Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Pinghua Qu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
| | - Ziping Wang
- Department of Thoracic Foncology, Peking University Cancer Hospital, Beijing, 100142, PR China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
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Effect of whole oilseeds in the diet on bacterial diversity in the solid fraction of the ruminal content of steers. Trop Anim Health Prod 2023; 55:32. [PMID: 36602697 DOI: 10.1007/s11250-022-03442-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023]
Abstract
Our hypothesis was that different whole oilseeds included in the diet for steers confined could alter the diversity of rumen bacteria compared to a diet without oilseeds or an exclusively forage diet. It was aimed to evaluate the effects of oilseeds inclusion in the diet on bacterial diversity in the solid fraction of the ruminal content of steers, by gene sequences of the conserved 16S rDNA region. Six crossbred steers castrated males, fitted with ruminal cannula were used in a 6 × 6 Latin square design, using 21-day period. At the start of the experiment, the live weight of the animals averaged 416 ± 9.7 kg (mean ± SD). A total of 2,180,562 16S rDNA sequences were generated for the Bacteria domain by MiSeq sequencing. The bacterial diversity was composed of 24 bacterial phyla, with the most abundant being Firmicutes, Bacteroidetes, and Proteobacteria. Other phyla with less diversity were also identified including Eurychaeota, Tenericutes, SR1 Absconditalbacteria, Synergistetes, Actinobacteria, Saccharibacteria, Elusimicrobia, Cyanobacteria, Verrucomicrobia, Fusobacteria, Lentisphaerae. The similarity in the bacterial community averaged 50% for all the experimental diets. Steers-fed corn silage exhibited a great diversity of bacteria of the Firmicutes phylum. The steers-fed oilseeds in the diet had a great diversity of bacteria from the phylum Bacteroidetes and Proteobacteria. The inclusion of whole oilseeds in the steer diets can alter the rumen bacteria population by up to 50% of total diversity.
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Choi Y, Lee SJ, Kim HS, Eom JS, Jo SU, Guan LL, Park T, Seo J, Lee Y, Bae D, Lee SS. Red seaweed extracts reduce methane production by altering rumen fermentation and microbial composition in vitro. Front Vet Sci 2022; 9:985824. [DOI: 10.3389/fvets.2022.985824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
A series of in vitro batch culture incubations were carried out to investigate changes in rumen fermentation characteristics, methane (CH4) production, and microbial composition in response to supplementation with five different red seaweed species (Amphiroa anceps, AANC; Asparagopsis taxiformis, ATAX; Chondracanthus tenellus, CTEN; Grateloupia elliptica, GELL; and Gracilaria parvispora, GPAR). Prior to the incubations, the total flavonoid and polyphenol content of the red seaweed extracts was quantified. The incubated substrate consisted of timothy hay and corn grain [60:40 dry matter (DM) basis]. Treatments were substrate mixtures without seaweed extract (CON) or substrate mixtures supplemented with 0.25 mg/mL of red seaweed extract. Samples were incubated for 6, 12, 24, 36, and 48 h. Each sample was incubated in triplicates in three separate runs. In vitro DM degradability, fermentation parameters (i.e., pH, volatile fatty acids, and ammonia nitrogen), total gas production, and CH4 production were analyzed for all time points. Microbial composition was analyzed using 16S rRNA amplicon sequencing after 24 h of incubation. The highest CH4 reduction (mL/g DM, mL/g digested DM, and % of total gas production) was observed in ATAX (51.3, 50.1, and 51.5%, respectively, compared to CON; P < 0.001) after 12 h of incubation. The other red seaweed extracts reduced the CH4 production (mL/g DM; P < 0.001) in the range of 4.6–35.0% compared to CON after 24 h of incubation. After 24 h of incubation, supplementation with red seaweed extracts tended to increase the molar proportion of propionate (P = 0.057) and decreased the acetate to propionate ratio (P = 0.033) compared to the CON. Abundances of the genus Methanobrevibacter and total methanogens were reduced (P = 0.050 and P = 0.016) by red seaweed extract supplementation. The linear discriminant analysis effect size (P < 0.05, LDA ≥ 2.0) showed that UG Succinivibrionaceae, Anaeroplasma, and UG Ruminococcaceae, which are associated with higher propionate production, starch degradation, and amylase activity were relatively more abundant in red seaweed extracts than in the CON. Our results suggest that supplementation with red seaweed extracts altered the microbiota, leading to the acceleration of propionate production and reduction in CH4 production.
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7
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Khomyakova MA, Zavarzina DG, Merkel AY, Klyukina AA, Pikhtereva VA, Gavrilov SN, Slobodkin AI. The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales. Front Microbiol 2022; 13:1047580. [PMID: 36439822 PMCID: PMC9686372 DOI: 10.3389/fmicb.2022.1047580] [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: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 08/01/2023] Open
Abstract
The continental subsurface harbors microbial populations highly enriched in uncultured taxa. OPB41 is an uncultured order-level phylogenetic lineage within the actinobacterial class Coriobacteriia. OPB41 bacteria have a wide geographical distribution, but the physiology and metabolic traits of this cosmopolitan group remain elusive. From two contrasting subsurface environments, a terrestrial mud volcano and a deep subsurface aquifer, located in the central part of Eurasia, within the Caucasus petroleum region, we have isolated two pure cultures of anaerobic actinobacteria belonging to OPB41. The cells of both strains are small non-motile rods forming numerous pili-like appendages. Strain M08DHBT is mesophilic, while strain Es71-Z0120T is a true thermophile having a broad temperature range for growth (25-77°C). Strain M08DHBT anaerobically reduces sulfur compounds and utilizes an aromatic compound 3,4-dihydroxybenzoic acid. Strain Es71-Z0120T is an obligate dissimilatory Fe(III) reducer that is unable to utilize aromatic compounds. Both isolates grow lithotrophically and consume molecular hydrogen or formate using either thiosulfate, elemental sulfur, or Fe(III) as an electron acceptor. Genomes of the strains encode the putative reductive glycine pathway for autotrophic CO2 fixation, Ni-Fe hydrogenases, putative thiosulfate/polysulfide reductases, and multiheme c-type cytochromes presumably involved in dissimilatory Fe(III) reduction. We propose to assign the isolated strains to the novel taxa of the species-order levels and describe strain M08DHBT as Anaerosoma tenue gen. nov., sp. nov., and strain Es71-Z0120T as Parvivirga hydrogeniphila gen. nov., sp. nov., being members of Anaerosomatales ord. nov. This work expands the knowledge of the diversity, metabolic functions, and ecological role of the phylum Actinomycetota.
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Affiliation(s)
- Maria A. Khomyakova
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I. Slobodkin
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Insect Gut Isolate Pseudomonas sp. Strain Nvir Degrades the Toxic Plant Metabolite Nitropropionic Acid. Appl Environ Microbiol 2022; 88:e0071922. [PMID: 36154165 PMCID: PMC9552603 DOI: 10.1128/aem.00719-22] [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] [Indexed: 11/20/2022] Open
Abstract
Nitropropionic acid (NPA) is a widely distributed naturally occurring nitroaliphatic toxin produced by leguminous plants and fungi. The Southern green shield bug feeds on leguminous plants and shows no symptoms of intoxication. Likewise, its gut-associated microorganisms are subjected to high levels of this toxic compound. In this study, we isolated a bacterium from this insect's gut system, classified as Pseudomonas sp. strain Nvir, that was highly resistant to NPA and was fully degrading it to inorganic nitrogen compounds and carbon dioxide. In order to understand the metabolic fate of NPA, we traced the fate of all atoms of the NPA molecule using isotope tracing experiments with [15N]NPA and [1-13C]NPA, in addition to experiments with uniformly 13C-labeled biomass that was used to follow the incorporation of 12C atoms from [U-12C]NPA into tricarboxylic acid cycle intermediates. With the help of genomics and transcriptomics, we uncovered the isolate’s NPA degradation pathway, which involves a putative propionate-3-nitronate monooxygenase responsible for the first step of NPA degradation. The discovered protein shares only 32% sequence identity with previously described propionate-3-nitronate monooxygenases. Finally, we advocate that NPA-degrading bacteria might find application in biotechnology, and their unique enzymes might be used in biosynthesis, bioremediation, and in dealing with postharvest NPA contamination in economically important products. IMPORTANCE Plants have evolved sophisticated chemical defense mechanisms, such as the production of plant toxins in order to deter herbivores. One example of such a plant toxin is nitropropionic acid (NPA), which is produced by leguminous plants and also by certain fungi. In this project, we have isolated a bacterium from the intestinal tract of a pest insect, the Southern green shield bug, that is able to degrade NPA. Through a multiomics approach, we identified the respective metabolic pathway and determined the metabolic fate of all atoms of the NPA molecule. In addition, we provide a new genetic marker that can be used for genome mining toward NPA degradation. The discovery of degradation pathways of plant toxins by environmental bacteria opens new possibilities for pretreatment of contaminated food and feed sources and characterization of understudied enzymes allows their broad application in biotechnology.
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Zhang G, Lv X, Cheng Y, Lai XH, Yang J, Jin D, Lu S, Pu J, Liu L, Xu J. New members of the family Eggerthellaceae isolated from Marmota himalayana: Xiamenia xianingshaonis gen. nov., sp. nov., from intestinal contents, and Berryella wangjianweii sp. nov., from trachea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886T/zg-887 and zg-1050T/zg-1084) were isolated from Marmota himalayana. Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family
Eggerthellaceae
: zg-1050T and zg-1084 were most closely related to
Berryella intestinalis
68-1-3T (97.2 %), while zg-886T/zg-887 had the highest similarity to
Slackia piriformis
YIT 12062T (91.6 %), followed by
Paraeggerthella hongkongensis
DSM 16106T (91.4 %) and
Gordonibacter urolithinfaciens
DSM 27213T (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family
Eggerthellaceae
. The genomic G+C contents of strains zg-886T and zg-1050T were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family
Eggerthellaceae
were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050T, strain zg-886T contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family
Eggerthellaceae
are proposed, Xiamenia xianingshaonis gen. nov., sp. nov. (zg-886T=JCM 34097T=GDMCC 1.1710T) and Berryella wangjianweii sp. nov. (zg-1050T=GDMCC 1.2426T=JCM 34748T).
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Affiliation(s)
- Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Xianglian Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yanpeng Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518073, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- Institute of Public Health, Nankai University, Tianjin 300071, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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Božic AK, Gutiérrez-Bañuelos H, Corral-Luna A, Carstens G, Arévalos-Sánchez MM, Félix-Portillo M, Muro-Reyes A, Arzola-Álvarez C, Anderson RC, Harvey RB. Dynamics of Gastrointestinal Activity and Ruminal Absorption of the Methane-Inhibitor, Nitroethane, in Cattle. Front Vet Sci 2022; 9:817270. [PMID: 35187146 PMCID: PMC8850640 DOI: 10.3389/fvets.2022.817270] [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: 11/17/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nitroethane is a potent methane-inhibitor for ruminants but little is known regarding simultaneous effects of repeated administration on pre- and post-gastric methane-producing activity and potential absorption and systemic accumulation of nitroethane in ruminants. Intraruminal administration of 120 mg nitroethane/kg body weight per day to Holstein cows (n = 2) over a 4-day period transiently reduced (P < 0.05) methane-producing activity of rumen fluid as much as 3.6-fold while concomitantly increasing (P < 0.05) methane-producing activity of feces by as much as 8.8-fold when compared to pre-treatment measurements. These observations suggest a bacteriostatic effect of nitroethane on ruminal methanogen populations resulting in increased passage of viable methanogens to the lower bovine gut. Ruminal VFA concentrations were also transiently affected by nitroethane administration (P < 0.05) reflecting adaptive changes in the rumen microbial populations. Mean (± SD) nitroethane concentrations in plasma of feedlot steers (n = 6/treatment) administered 80 or 160 mg nitroethane/kg body weight per day over a 7-day period were 0.12 ± 0.1 and 0.41 ± 0.1 μmol/mL 8 h after the initial administration indicating rapid absorption of nitroethane, with concentrations peaking 1 day after initiation of the 80 or 160 mg nitroethane/kg body weight per day treatments (0.38 ± 0.1 and 1.14 ± 0.1 μmol/mL, respectively). Plasma nitroethane concentrations declined thereafter to 0.25 ± 0.1 and 0.78 ± 0.3 and to 0.18 ± 0.1 and 0.44 ± 0.3 μmol/mL on days 2 and 7 for the 80 or 160 mg nitroethane/kg body weight per day treatment groups, respectively, indicating decreased absorption due to increased ruminal nitroethane degradation or to more rapid excretion of the compound.
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Affiliation(s)
- Aleksandar K. Božic
- Faculty of Agriculture, Department of Animal Science, University of Novi Sad, Novi Sad, Serbia
| | - Hector Gutiérrez-Bañuelos
- Unidad Académica de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Agustin Corral-Luna
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Gordon Carstens
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | | | | | - Alberto Muro-Reyes
- Unidad Académica de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | | | - Robin C. Anderson
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Roger B. Harvey
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, United States
- *Correspondence: Roger B. Harvey
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11
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Li Y, Kreuzer M, Clayssen Q, Ebert MO, Ruscheweyh HJ, Sunagawa S, Kunz C, Attwood G, Amelchanka S, Terranova M. The rumen microbiome inhibits methane formation through dietary choline supplementation. Sci Rep 2021; 11:21761. [PMID: 34741032 PMCID: PMC8571420 DOI: 10.1038/s41598-021-01031-w] [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: 06/20/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022] Open
Abstract
Enteric fermentation from ruminants is a primary source of anthropogenic methane emission. This study aims to add another approach for methane mitigation by manipulation of the rumen microbiome. Effects of choline supplementation on methane formation were quantified in vitro using the Rumen Simulation Technique. Supplementing 200 mM of choline chloride or choline bicarbonate reduced methane emissions by 97–100% after 15 days. Associated with the reduction of methane formation, metabolomics analysis revealed high post-treatment concentrations of ethanol, which likely served as a major hydrogen sink. Metagenome sequencing showed that the methanogen community was almost entirely lost, and choline-utilizing bacteria that can produce either lactate, ethanol or formate as hydrogen sinks were enriched. The taxa most strongly associated with methane mitigation were Megasphaera elsdenii and Denitrobacterium detoxificans, both capable of consuming lactate, which is an intermediate product and hydrogen sink. Accordingly, choline metabolism promoted the capability of bacteria to utilize alternative hydrogen sinks leading to a decline of hydrogen as a substrate for methane formation. However, fermentation of fibre and total organic matter could not be fully maintained with choline supplementation, while amino acid deamination and ethanolamine catabolism produced excessive ammonia, which would reduce feed efficiency and adversely affect live animal performance.
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Affiliation(s)
- Yang Li
- Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
| | - Michael Kreuzer
- Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Quentin Clayssen
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Marc-Olivier Ebert
- Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | | | - Shinichi Sunagawa
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Carmen Kunz
- Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Graeme Attwood
- AgResearch Ltd. Grasslands Research Centre, Palmerston North, 4442, New Zealand
| | - Sergej Amelchanka
- ETH Zurich, AgroVet-Strickhof, Eschikon 27, 8315, Lindau, Switzerland
| | - Melissa Terranova
- ETH Zurich, AgroVet-Strickhof, Eschikon 27, 8315, Lindau, Switzerland
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12
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Astragallus mollissimus plant extract: a strategy to reduce ruminal methanogenesis. Trop Anim Health Prod 2021; 53:436. [PMID: 34401959 DOI: 10.1007/s11250-021-02882-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Ruminal methanogenesis is considered an inefficient process as it can result in the loss of 4 to 12% of the total energy consumed by the ruminant. Recent studies have shown that compounds such as nitroethane, 2-nitroethanol, 2-nitro-1-propanol, and 3-nitro-1-propionic acid are capable of inhibiting methane production during in vitro studies. However, all of these nitrocompounds came from a synthetic origin, which could limit their use. In contrast, some plants of the Astragallus genus produce a natural nitrocompound, although its anti-methanogenic effect has not been evaluated. To determine the anti-methanogenic effect, in vitro cultures of freshly collected mixed populations of ruminal microbes were supplemented with A. mollissimus extracts (MISER). Cultures supplemented with 2-nitroethanol, ethyl 2-nitroacetate, or nitroethane were used as positive controls whereas distilled water was added to the untreated control tubes. After a 24 h incubation period, the methane production was reduced by more than 98% for the samples treated with A. mollissimus extract (P < 0.05) compared to the untreated controls (10.2 ± 0.1 mmol mL-1 incubated liquid). Cultures supplemented with MISER produced a greater (P < 0.05) amount of total VFA, compared to the rest of treated and untreated cultures. Considering that there are significant differences between MISER treatment, positive controls and untreated cultures (P < 0.05) regarding the amounts of total gas, gas composition (CH4 and H2), and the amount of VFA produced, it is concluded that Astragallus mollissimus poses an alternative strategy to reduce ruminal methanogenesis. To further explore such alternative, it is necessary to determine if the metabolization byproducts are safe and/or useful for the animal.
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13
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Teng PY, Kim WK. Roles of Nitrocompounds in Inhibition of Foodborne Bacteria, Parasites, and Methane Production in Economic Animals. Animals (Basel) 2021; 11:ani11040923. [PMID: 33805112 PMCID: PMC8064083 DOI: 10.3390/ani11040923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/20/2021] [Accepted: 03/21/2021] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Supplementation of nitrocompounds in animal diets has been studied to investigate their effects on economic animals. It has been known that nitrocompounds are capable of inhibiting pathogens, parasites, methane and ammonia production. The toxicity, metabolism, and mechanisms of actions have been discussed in the review to conclude the advantages and disadvantages of application of nitrocompounds in animal production. Abstract Nitrocompounds are derivatives of hydrocarbons, alcohols, fatty acids, and esters, consisting one or more nitro functional groups. Either natural sources of nitrocompounds or synthetic chemicals have been applied in animal diets to investigate their effects on economic animals, since conjugates of 3-nitropropanol and 3-nitropropionic acid were isolated from Astragalus oblongifolius. In this review, emphasis will be placed on nitrocompounds’ antimicrobial activity, toxicity, metabolisms and mechanisms of actions. Nitrocompounds can be metabolized by ruminal microbials, such as Denitrobacterium detoxificans, or alcohol dehydrogenase in the liver. Moreover, it has been found that nitrocompounds are capable of inhibiting pathogens, parasites, methane and ammonia production; however, overdose of nitrocompounds could cause methemoglobinemia or interfere with energy production in mitochondria by inhibiting succinate dehydrogenase.
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14
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He X, Yin H, Fang C, Xiong J, Han L, Yang Z, Huang G. Metagenomic and q-PCR analysis reveals the effect of powder bamboo biochar on nitrous oxide and ammonia emissions during aerobic composting. BIORESOURCE TECHNOLOGY 2021; 323:124567. [PMID: 33401162 DOI: 10.1016/j.biortech.2020.124567] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
To investigate the emission mechanism of ammonia (NH3) and nitrous oxide (N2O) during aerobic composting and the influence of powder bamboo biochar (PBB) on this process, this paper conducted a systematic study on the nitrogen-transforming functional microbial community, including functional genes, microbial structure and metabolism pathways. PBB reduced N2O and NH3 emissions by 1.25%-8.72% and 10.4%-11.8%, respectively. The quantitative PCR results indicated that the reduced N2O emission by PBB were mainly related to denitrifying genes (nirS, nirK, nosZ, and narG). The metagenome results demonstrated that Nitrosococcus was the main genus that could oxidize ammonia to nitrite decreased by PBB. The PBB significantly affected the nitrogen metabolism pathway, reduced the activity of glutamate dehydrogenase to inhibit the formation of NH4+ to reduce NH3 emission. The higher N2O emission in the control group was also related to the higher relative contents of hydroxylamine reductase and nitrite reductase.
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Affiliation(s)
- Xueqin He
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Hongjie Yin
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Chen Fang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Jinpeng Xiong
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Lujia Han
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Zengling Yang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China
| | - Guangqun Huang
- Engineering Laboratory for Agrobiomass Recycling & Valorizing, China Agricultural University, Beijing 100083, China.
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15
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Ruiz-Barrera O, Ontiveros-Magadan M, Anderson RC, Byrd JA, Hume ME, Latham EA, Nisbet DJ, Arzola-Alvarez C, Salinas-Chavira J, Castillo-Castillo Y. Nitro-treatment of composted poultry litter; effects on Salmonella, E. coli and nitrogen metabolism. BIORESOURCE TECHNOLOGY 2020; 310:123459. [PMID: 32389429 DOI: 10.1016/j.biortech.2020.123459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Poultry litter is a potentially valuable crude protein feedstuff for ruminants but must be treated to kill pathogens before being fed. Composting kills pathogens but risks losses of nitrogen due to volatilization or leaching as ammonia. Treatment of poultry litter with ethyl nitroacetate, 3-nitro-1-propionate, ethyl 2-nitropropionate (at 27 µmol/g), decreased numbers of experimentally-inoculated Salmonella Typhimurium (>1.0 log10 compared to controls, 4.2 ± 0.2 log10 CFU/g) but not endogenous Escherichia coli early during simulated composting. By day 9 of simulated composting, Salmonella and E. coli were decreased to non-detectable levels regardless of treatment. Some nitro-treatments preserved uric acid and prevented ammonia accumulation, with 18% more uric acid remaining and 17-24% less ammonia accumulating in some nitro-treated litter than in untreated litter (18.1 ± 3.8 µmol/g and 3.4 ± 1.4 µmol/g, respectively). Results indicate that nitro-treatment may help preserve uric acid in composted litter while aiding Salmonella control.
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Affiliation(s)
| | | | - Robin C Anderson
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Service, Food and Feed Safety Research Unit, College Station, TX, USA
| | - J Allen Byrd
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Service, Food and Feed Safety Research Unit, College Station, TX, USA
| | - Michael E Hume
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Service, Food and Feed Safety Research Unit, College Station, TX, USA
| | | | - David J Nisbet
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Service, Food and Feed Safety Research Unit, College Station, TX, USA
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16
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Zhang Z, Wang Y, Si X, Cao Z, Li S, Yang H. Rumen Methanogenesis, Rumen Fermentation, and Microbial Community Response to Nitroethane, 2-Nitroethanol, and 2-Nitro-1-Propanol: An In Vitro Study. Animals (Basel) 2020; 10:ani10030479. [PMID: 32182983 PMCID: PMC7143717 DOI: 10.3390/ani10030479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/01/2020] [Accepted: 03/05/2020] [Indexed: 11/16/2022] Open
Abstract
Nitroethane (NE), 2-nitroethanol (NEOH), and 2-nitro-1-propanol (NPOH) were comparatively examined to determine their inhibitory actions on rumen fermentation and methanogenesis in vitro. Fermentation characteristics, CH4 and total gas production, and coenzyme contents were determined at 6, 12, 24, 48, and 72 h incubation time, and the populations of ruminal microbiota were analyzed by real-time PCR at 72 h incubation time. The addition of NE, NEOH, and NPOH slowed down in vitro rumen fermentation and reduced the proportion of molar CH4 by 96.7%, 96.7%, and 41.7%, respectively (p < 0.01). The content of coenzymes F420 and F430 and the relative expression of the mcrA gene declined with the supplementation of NE, NEOH, and NPOH in comparison with the control (p < 0.01). The addition of NE, NEOH, and NPOH decreased total volatile fatty acids (VFAs) and acetate (p < 0.05), but had no effect on propionate concentration (p > 0.05). Real-time PCR results showed that the relative abundance of total methanogens, Methanobacteriales, Methanococcales, and Fibrobacter succinogenes were reduced by NE, NEOH, and NPOH (p < 0.05). In addition, the nitro-degradation rates in culture fluids were ranked as NEOH (-0.088) > NE (-0.069) > NPOH (-0.054). In brief, the results firstly provided evidence that NE, NEOH, and NPOH were able to decrease methanogen abundance and dramatically decrease mcrA gene expression and coenzyme F420 and F430 contents with different magnitudes to reduce ruminal CH4 production.
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17
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Zhang ZW, Wang YL, Wang WK, Chen YY, Si XM, Wang YJ, Wang W, Cao ZJ, Li SL, Yang HJ. The Antimethanogenic Nitrocompounds Can be Cleaved into Nitrite by Rumen Microorganisms: A Comparison of Nitroethane, 2-Nitroethanol, and 2-Nitro-1-propanol. Metabolites 2019; 10:E15. [PMID: 31881649 PMCID: PMC7023367 DOI: 10.3390/metabo10010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
A class of aliphatic short chain nitrocompounds have been reported as being capable of CH4 reduction both in vitro and in vivo. However, the laboratory evidence associated with the metabolic fate of nitrocompounds in the rumen has not been well documented. The present study was conducted to compare in vitro degradation and metabolism of nitroethane (NE), 2-nitroethanol (NEOH), and 2-nitro-1-propanol (NPOH) incubated with mixed rumen microorganisms of dairy cows. After 10 mM supplementation of nitrocompounds, a serious of batch cultures were carried out for 120 h under the presence of two substrates differing in the ratio of maize meal to alfalfa hay (HF, 1:4; LF, 4:1). Compared to the control, methane production was reduced by 59% in NPOH and by >97% in both NE and NEOH, and such antimethanogenic effects were more pronounced in the LF than the HF group. Although NE, NEOH, and NPOH addition did not alter total VFA production, the rumen fermentation pattern shifted toward increasing propionate and butyrate and decreasing acetate production. The kinetic disappearance of each nitrocompound was well fitted to the one-compartment model, and the disappearance rate (k, %/h) of NE was 2.6 to 5.2 times greater than those of NEOH and NPOH. Higher intermediates of nitrite occurred in NEOH in comparison with NPOH and NE while ammonia N production was lowest in NEOH. Consequently, a stepwise accumulation of bacterial crude protein (BCP) in response to the nitrocompound addition was observed in both the HF and LF group. In brief, both NE and NEOH in comparison with NPOH presented greater antimethanogenic activity via the shift of rumen fermentation. In addition, the present study provided the first direct evidence that rumen microbes were able to cleave these nitrocompounds into nitrite, and the subsequent metabolism of nitrite into ammonia N may enhance the growth of rumen microbes or promote microbial activities.
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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; (Z.-W.Z.); (Y.-L.W.); (W.-K.W.); (Y.-Y.C.); (X.-M.S.); (Y.-J.W.); (W.W.); (Z.-J.C.); (S.-L.L.)
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18
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Deng S, Yan X, Zhu Q, Liao C. The utilization of reclaimed water: Possible risks arising from waterborne contaminants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113020. [PMID: 31421574 DOI: 10.1016/j.envpol.2019.113020] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/11/2019] [Accepted: 08/04/2019] [Indexed: 05/04/2023]
Abstract
Increasing interest of seeking substitutable water resources accrues from shortage of freshwater. One of the options considered is reclaimed water (also designated as recycled water) that has been widely used in daily life. Although reclaimed water can serve as a feasible reliever of water pressure, attention about its technologies and potential risks is growing in the meantime. Most established wastewater treatment plants (WWTPs) predate many new contaminants, which means treatment processes cannot ensure to dislodge certain contaminants completely from origin water. Furthermore, a wide range of factors, such as seasons and influent variations, affect occurrence and concentration of reclaimed water-borne contaminants, making research about quality of reclaimed water especially significant. Many reclaimed water-borne contaminants, including biological and chemical contaminants, are toxic to human health, and complex wastewater matrix may aggravate water quality of concern. The widespread use of reclaimed water continues to be a concern on agriculture, ecological environment and human health. This study aims to: 1) provide a critical review about occurrence and profiles of diverse contaminants in the treated reclaimed water, 2) discuss the possibility to avoid the secondary pollution in reuse of reclaimed water, and 3) reveal the prospective consequences of using reclaimed water on agriculture, ecological environment and human health.
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Affiliation(s)
- Shenxi Deng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Liao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China.
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19
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Toluene degradation via a unique metabolic route in indigenous bacterial species. Arch Microbiol 2019; 201:1369-1383. [PMID: 31332474 DOI: 10.1007/s00203-019-01705-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/27/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022]
Abstract
Tanneries are the primary source of toluene pollution in the environment and toluene due to its hazardous effects has been categorized as persistent organic pollutant. Present study was initiated to trace out metabolic fingerprints of three toluene-degrading bacteria isolated from tannery effluents of Southern Punjab. Using selective enrichment and serial dilution methods followed by biochemical, molecular and antibiotic resistance analysis, isolated bacteria were subjected to metabolomics analysis. GC-MS/LC-MS analysis of bacterial metabolites helped to identify toluene transformation products and underlying pathways. Three toluene-metabolizing bacteria identified as Bacillus paralicheniformis strain KJ-16 (IUBT4 and IUBT24) and Brevibacillus agri strain NBRC 15538 (IUBT19) were found tolerant to toluene and capable of degrading toluene. Toluene-degrading potential of these isolates was detected to be IUBT4 (10.35 ± 0.084 mg/h), IUBT19 (14.07 ± 3.14 mg/h) and IUBT24 (11.1 ± 0.282 mg/h). Results of GC-MS analysis revealed that biotransformation of toluene is accomplished not only through known metabolic routes such as toluene 3-monooxygenase (T3MO), toluene 2-monooxygenase (T2MO), toluene 4-monooxygenase (T4MO), toluene methyl monooxygenase (TOL), toluene dioxygenase (Tod), meta- and ortho-ring fission pathways. But additionally, confirmed existence of a unique metabolic pathway that involved conversion of toluene into intermediates such as cyclohexene, cyclohexane, cyclohexanone and cyclohexanol. LC-MS analysis indicated the presence of fatty acid amides, stigmine, emmotin A and 2, 2-dinitropropanol in supernatants of bacterial cultures. As the isolated bacteria transformed toluene into relatively less toxic molecules and thus can be preferably exploited for the eco-friendly remediation of toluene.
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20
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Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME JOURNAL 2019; 13:2617-2632. [PMID: 31243332 PMCID: PMC6776011 DOI: 10.1038/s41396-019-0464-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 01/17/2023]
Abstract
Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.
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Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Renae Geier
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cecilia Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura C Woods
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Rowena Rushton-Green
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | | | - Isaac Cann
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graeme T Attwood
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD, Tall ML, Michelle C, Yasir M, Ibraheem Azhar E, Bibi F, Bittar F, Jiman‐Fatani AA, Daoud Z, Cadoret F, Fournier P, Edouard S. Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut. Microbiologyopen 2019; 8:e00758. [PMID: 30701700 PMCID: PMC6562231 DOI: 10.1002/mbo3.758] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.
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Affiliation(s)
- Sory Ibrahima Traore
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Melhem Bilen
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
- Clinical Microbiology Department, Faculty of Medicine and Medical sciencesUniversity of BalamandAmiounLebanon
| | - Mamadou Beye
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Awa Diop
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | | | - Mamadou Lamine Tall
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Caroline Michelle
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
- Medical Laboratory Technology Department, Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fadi Bittar
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Asif Ahmad Jiman‐Fatani
- Department of Medical Microbiology and Parasitology, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Ziad Daoud
- Department of Medical Microbiology and Parasitology, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fréderic Cadoret
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Pierre‐Edouard Fournier
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Sophie Edouard
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
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Ochoa-García PA, Arevalos-Sánchez MM, Ruiz-Barrera O, Anderson RC, Maynez-Pérez AO, Rodríguez-Almeida FA, Chávez-Martínez A, Gutiérrez-Bañuelos H, Corral-Luna A. In vitro reduction of methane production by 3-nitro-1-propionic acid is dose-dependent1. J Anim Sci 2019; 97:1317-1324. [PMID: 30649418 DOI: 10.1093/jas/skz012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/08/2019] [Indexed: 11/12/2022] Open
Abstract
Methanogenesis is a metabolic process that allows the rumen ecosystem the ability to maintain the low hydrogen partial pressures needed for proper digestive function. However, rumen methanogenesis is considered to be an inefficient process because it can result in the loss of 4% to 12% of the total energy consumed by the host. Recent studies have shown that some short-chain nitrocompounds such as nitroethane, 2-nitroethanol, 2-nitro-1-propanol, and 3-nitro-1-propionic acid (3NPA) are capable of inhibiting the production of methane during in vitro culture; nevertheless, optimal supplementation doses have yet to be determined. In the present study, in vitro cultures of freshly collected mixed populations of ruminal microbes were supplemented with the naturally occurring nitrocompound, 3NPA, to achieve 0, 3, 6, 9, or 12 mM. Analysis of fermentation products after 24 h of incubation revealed that methane (CH4) production was reduced in a dose-dependent manner by 29% to 96% (P < 0.05) compared with the amount produced by untreated controls (15.03 ± 0.88 µmol mL-1 incubated liquid). Main effects of the supplement were also observed, which resulted in a reduction (P < 0.05) on amounts of total gas and volatile fatty acids (VFA) produced, as well as in an increase of 0.07 to 0.30 µmol mL-1 on rates of 3NPA degradation. Changes in production of metabolites as CH4, hydrogen (H2), VFA, and NH3 indicated that the fermentation efficiency was not compromised dramatically by 3NPA treatment in moderate doses of 6 and 9 mM. Results further revealed that the metabolism of the 3NPA by microbial populations is also dose-dependent. The microbes were able to metabolize more than 75% of the added nitrocompound, with the greatest degradation rates in cultures treated with 9-mM 3NPA. Finally, from a practical standpoint, and considering the magnitude of CH4 reduction, effect on VFA, and percentage of metabolized supplement, the most efficacious dose for 3NPA administration may be between 3 and 9 mM.
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Affiliation(s)
- Pedro Antonio Ochoa-García
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - Martha María Arevalos-Sánchez
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - Oscar Ruiz-Barrera
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - Robin C Anderson
- USDA/ARS, Food and Feed Safety Research Unit, College Station, TX
| | - Adrián Omar Maynez-Pérez
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - Felipe A Rodríguez-Almeida
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - América Chávez-Martínez
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
| | - Héctor Gutiérrez-Bañuelos
- Unidad Académica de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Agustín Corral-Luna
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chih. México, Chihuahua, Chihuahua, México
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23
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Božić A, Anderson RC, Arzola-Alvarez C, Ruiz-Barrera O, Corral-Luna A, Castillo-Castillo Y, Arzola-Rubio A, Poole TL, Harvey RB, Hume ME, Beier RC, Nisbet DJ. Inhibition of multidrug-resistant Staphylococci by sodium chlorate and select nitro- and medium chain fatty acid compounds. J Appl Microbiol 2019; 126:1508-1518. [PMID: 30803130 DOI: 10.1111/jam.14232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/28/2022]
Abstract
AIMS Determine the antimicrobial effects of 5 μmol ml-1 sodium chlorate, 9 μmol ml-1 nitroethane or 2-nitropropanol as well as lauric acid, myristic acid and the glycerol ester of lauric acid Lauricidin® , each at 5 mg ml-1 , against representative methicillin-resistant staphylococci, important mastitis- and opportunistic dermal-pathogens of humans and livestock. METHODS AND RESULTS Three methicillin-resistant Staphylococcus aureus and two methicillin-resistant coagulase-negative staphylococci were cultured at 39°C in 5 μmol ml-1 nitrate-supplemented half-strength Brain Heart Infusion broth treated without or with the potential inhibitors. Results revealed that 2-nitropropanol was the most potent and persistent of all compounds tested, achieving 58-99% decreases in mean specific growth rates and maximum optical densities when compared with untreated controls. Growth inhibition did not persist by cultures treated solely with chlorate or nitroethane, with adaptation occurring by different mechanisms after 7 h. Adaptation did not occur in cultures co-treated with nitroethane and chlorate. The medium chain fatty acid compounds had modest effects on all the staphylococci tested except the coagulase-negative Staphylococcus epidermidis strain NKR1. CONCLUSIONS The antimicrobial activity of nitrocompounds, chlorate and medium chain fatty acid compounds against different methicillin-resistant staphylococci varied in potency. SIGNIFICANCE AND IMPACT OF THE STUDY Results suggest that differential antimicrobial activities exhibited by mechanistically dissimilar inhibitors against methicillin-resistant staphylococci may yield potential opportunities to combine the treatments to overcome their individual limitations and broaden their activity against other mastitis and dermal pathogens.
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Affiliation(s)
- A Božić
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - R C Anderson
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - C Arzola-Alvarez
- College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - O Ruiz-Barrera
- College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - A Corral-Luna
- College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Y Castillo-Castillo
- College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - A Arzola-Rubio
- College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - T L Poole
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - R B Harvey
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - M E Hume
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - R C Beier
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - D J Nisbet
- United States Department of Agriculture/Agricultural Research Service, Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, College Station, TX, USA
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Changes in the Rumen Microbiota of Cows in Response to Dietary Supplementation with Nitrate, Linseed, and Saponin Alone or in Combination. Appl Environ Microbiol 2019; 85:AEM.02657-18. [PMID: 30504215 DOI: 10.1128/aem.02657-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 01/21/2023] Open
Abstract
Dietary supplementation with linseed, saponins, and nitrate is a promising methane mitigation strategy in ruminant production. Here, we aimed to assess the effects of these additives on the rumen microbiota in order to understand underlying microbial mechanisms of methane abatement. Two 2-by-2 factorial design studies were conducted simultaneously, which also allowed us to make a broad-based assessment of microbial responses. Eight nonlactating cows were fed diets supplemented with linseed or saponin in order to decrease hydrogen production and nitrate to affect hydrogen consumption; also, combinations of linseed plus nitrate or saponin plus nitrate were used to explore the interaction between dietary treatments. Previous work assessed effects on methane and fermentation patterns. Rumen microbes were studied by sequencing 18S and 16S rRNA genes and ITS1 amplicons. Methanogen activity was monitored by following changes in mcrA transcript abundance. Nitrate fed alone or in combination in both studies dramatically affected the composition and structure of rumen microbiota, although impacts were more evident in one of the studies. Linseed moderately modified only bacterial community structure. Indicator operational taxonomic unit (OTU) analysis revealed that both linseed and nitrate reduced the relative abundance of hydrogen-producing Ruminococcaceae Linseed increased the proportion of bacteria known to reduce succinate to propionate, whereas nitrate supplementation increased nitrate-reducing bacteria and decreased the metabolic activity of rumen methanogens. Saponins had no effect on the microbiota. Inconsistency found between the two studies with nitrate supplementation could be explained by changes in microbial ecosystem functioning rather than changes in microbial community structure.IMPORTANCE This study aimed at identifying the microbial mechanisms of enteric methane mitigation when linseed, nitrate, and saponins were fed to nonlactating cows alone or in a combination. Hydrogen is a limiting factor in rumen methanogenesis. We hypothesized that linseed and saponins would affect hydrogen producers and nitrate would affect hydrogen consumption, leading to reduced methane production in the rumen. Contrary to what was predicted, both linseed and nitrate had a deleterious effect on hydrogen producers; linseed also redirected hydrogen consumption toward propionate production, whereas nitrate stimulated the growth of nitrate-reducing and, hence, hydrogen-consuming bacterial taxa. This novel knowledge of microbial mechanisms involved in rumen methanogenesis provides insights for the development and optimization of methane mitigation strategies.
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Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach. Antonie van Leeuwenhoek 2019; 112:775-784. [PMID: 30666529 DOI: 10.1007/s10482-018-01211-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/01/2018] [Indexed: 10/27/2022]
Abstract
Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human gut microbiota by culturomics, Phoenicibacter congonensis strain Marseille-P3241T was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241T is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241T is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of Denitrobacterium detoxificans strain NPOH1T, the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241T (= CCUG 70681T = CSUR P3241T) represents the type species of a new genus, for which we propose the name Phoenicibacter congonensis gen. nov., sp. nov.
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Wan R, Wang L, Chen Y, Zheng X, Su Y, Tao X. Insight into a direct carbon dioxide effect on denitrification and denitrifying bacterial communities in estuarine sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1074-1083. [PMID: 30189524 DOI: 10.1016/j.scitotenv.2018.06.279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
With the elevation of atmospheric CO2 content, the potential effects of CO2 on organisms and various environmental processes have gained increasing concern. Most previous studies on denitrification have been conducted on ecosystems comprising plants, soils and microbes, but they have ignored the direct effect of CO2 on denitrification and denitrifying bacterial communities. Here, by excluding the effects of plants, we found that both short- and long-term exposure to CO2 directly inhibited the denitrification process, and caused the total nitrogen removal efficiency to decrease by up to 37%. Compared with the control, long-term exposure to CO2 (30,000 ppm) also caused >276-fold increase in N2O emissions, and significantly inhibited the decomposition process. Enzymatic and qPCR assays showed that CO2 decreased the denitrifying enzymes activity (DEA) and the copy numbers of denitrifying genes, which directly resulted in the inhibitory effect of CO2 on denitrification process. Further study indicated that adverse effect of CO2 on DEA and denitrifying genes were caused by reducing the relative abundance of denitrifying bacteria. Moreover, the relative abundance of fermenting bacteria also decreased as CO2 concentration increased, which might result in insufficient liable carbon for the activity of denitrifying bacteria, and ultimately exacerbate the negative denitrification performance. Overall, this study suggests that, in the absence of plants, CO2 could directly affect the denitrifying and fermenting bacterial community, and inhibit denitrification and decomposition processes, which is detrimental to sediment nitrogen and carbon cycles.
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Affiliation(s)
- Rui Wan
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China; State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lei Wang
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiucheng Tao
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China
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Matturro B, Pierro L, Frascadore E, Petrangeli Papini M, Rossetti S. Microbial Community Changes in a Chlorinated Solvents Polluted Aquifer Over the Field Scale Treatment With Poly-3-Hydroxybutyrate as Amendment. Front Microbiol 2018; 9:1664. [PMID: 30087670 PMCID: PMC6066499 DOI: 10.3389/fmicb.2018.01664] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/04/2018] [Indexed: 12/18/2022] Open
Abstract
This study investigated the organohalide-respiring bacteria (OHRB) and the supporting microbial populations operating in a pilot scale plant employing poly-3-hydroxybutyrate (PHB), a biodegradable polymer produced by bacteria from waste streams, for the in situ bioremediation of groundwater contaminated by chlorinated solvents. The bioremediation was performed in ground treatment units, including PHB reactors as slow release source of electron donors, where groundwater extracted from the wells flows through before the re-infiltration to the low permeability zones of the aquifer. The coupling of the biological treatment with groundwater recirculation allowed to drastically reducing the contamination level and the remediation time by efficiently stimulating the growth of autochthonous OHRB and enhancing the mobilization of the pollutants. Quantitative PCR performed along the external treatment unit showed that the PHB reactor may efficiently act as an external incubator to growing Dehalococcoides mccartyi, known to be capable of fully converting chlorinated ethenes to innocuous end-products. The slow release source of electron donors for the bioremediation process allowed the establishment of a stable population of D. mccartyi, mainly carrying bvcA and vcrA genes which are implicated in the metabolic conversion of vinyl chloride to harmless ethene. Next generation sequencing was performed to analyze the phylogenetic diversity of the groundwater microbiome before and after the bioremediation treatment and allowed the identification of the microorganisms working closely with organohalide-respiring bacteria.
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Affiliation(s)
| | - Lucia Pierro
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
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Shaani Y, Zehavi T, Eyal S, Miron J, Mizrahi I. Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects. ISME JOURNAL 2018; 12:2446-2457. [PMID: 29921849 DOI: 10.1038/s41396-018-0203-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/05/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022]
Abstract
Niche modification is a process whereby the activity of organisms modifies their local environment creating new niches for other organisms. This process can have a substantial role in community assembly of gut microbial ecosystems due to their vast and complex metabolic activities. We studied the postprandial diurnal community oscillatory patterns of the rumen microbiome and showed that metabolites produced by the rumen microbiome condition its environment and lead to dramatic diurnal changes in community composition and function. After feeding, microbiome composition undergoes considerable change in its phylogenetic breadth manifested as a significant 3-5-fold change in the relative abundance of methanogenic archaea and main bacterial taxa such as Prevotella, in a manner that was independent of individual host variation and diet. These changes in community composition were accompanied by changes in pH and methane partial pressure, suggesting a strong functional connection. Notably, cross-incubation experiments combining metabolites and organisms from different diurnal time points showed that the metabolites released by microbes are sufficient to reproduce changes in community function comparable to those observed in vivo. These findings highlight microbiome niche modification as a deterministic process that drives diurnal community assembly via environmental filtering.
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Affiliation(s)
- Yoav Shaani
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, 7 Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel.,Department of Cattle Husbandry, Extension Service, Ministry of Agriculture, PO Box 28, Bet-Dagan, 50250, Israel
| | - Tamar Zehavi
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, 7 Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Stav Eyal
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, 7 Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Joshuah Miron
- Department of Ruminant Science, Institute of Animal Science, Agricultural Research Organization, PO Box 6, Bet-Dagan, 50250, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, 7 Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel.
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Danylec N, Göbl A, Stoll DA, Hetzer B, Kulling SE, Huch M. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 2018. [PMID: 29537365 DOI: 10.1099/ijsem.0.002705] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel, anaerobic, Gram-positive, rod-shaped bacterial strains, ResAG-85T and ResAG-96T, were isolated from a faecal sample of a male human. 16S rRNA gene sequences analyses indicated that these strains represent a distinct lineage within the family Eggerthellaceae. Strain ResAG-85T showed 92.3 % similarity to the type strains of the genera Eggerthella and Gordonibacter. Strain ResAG-96T clustered together with Paraeggerthella hongkongensis and the newly (but not validly) published genus 'Arabia massiliensis' (94.8 % similarity). Analysis of quinones revealed that MK-5 (21 % in ResAG-85T and 95 % in ResAG-96T) and MK-7 (53 % in strain ResAG-85T) were present, which were described for the first time for members of the Eggerthellaceae. Furthermore, MK-6 was present in both strains (25 % ResAG-85T and 5 % in ResAG-96T). The polar lipids detected in ResAG-85T and ResAG-96T consisted of eight and six glycolipids, respectively. Both strains possessed three phospholipids, one phosphatidylglycerol and one diphosphatidylglycerol. Analysis of fatty acids revealed that the percentage of total branched fatty acids was relatively high in comparison to related strains with 42 and 50 % of strains ResAG-85T and ResAG-96T but comparable to the value obtained for Gordonibacter pamelaeae DSM 19378T. On the basis of this polyphasic approach including molecular (16S rRNA gene sequencing) and biochemical methods (analysis of fatty acids, quinones, polar lipids, Rapid ID 32A and API 20A), the new genera and species Rubneribacter badeniensis with ResAG-85T (=DSM 105129T=JCM 32272T) and Enteroscipio rubneri with ResAG-96T (=DSM 105130T=JCM 32273T) as the type and only strains are described.
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Affiliation(s)
- Nicolas Danylec
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Andrea Göbl
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
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Elsawi Z, Togo AH, Beye M, Dubourg G, Andrieu C, Armsrtong N, Richez M, di Pinto F, Bittar F, Labas N, Fournier PE, Raoult D, Khelaifia S. Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut. Microbiologyopen 2017; 6. [PMID: 28326685 PMCID: PMC5552949 DOI: 10.1002/mbo3.458] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 12/19/2022] Open
Abstract
The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI‐TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8T (=CSUR P2118 = DSM 101782) from stool specimens collected from a 51‐year‐old obese French woman. Strain AT8T is a strictly anaerobic, nonmotile, nonspore‐forming gram‐positive coccus that do not exhibit catalase and oxidase activities. 16S rDNA‐based identification of strain AT8T demonstrated 92% gene sequence similarity with Eggerthella lenta DSM 2243, the phylogenetically closed validly named type species. Here, we present a set of features for the strain AT8T and the description of its complete genome sequence and annotation. The 2,091,845 bp long genome has a G+C content of 63.46% and encodes1,849 predicted genes; 1,781 were protein‐coding genes, and 68 were RNAs. On the basis of the characteristics reported here, we propose the creation of a new bacterial genus Hugonella gen. nov., belonging to the Eggerthellaceae family and including Hugonella massiliensis gen. nov., sp. nov., strain AT8T as the type strain.
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Affiliation(s)
- Ziena Elsawi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Amadou Hamidou Togo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Mamadou Beye
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Grégory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Nicholas Armsrtong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Magali Richez
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Fabrizio di Pinto
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Fadi Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Noémie Labas
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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Ruiz-Barrera O, Anderson RC, Hume ME, Corrales-Millan J, Castillo-Castillo Y, Corral-Luna A, Guevara-Valdez JL, Salinas-Chavira J, Rodriguez-Muela C, Arzola-Alvarez C. Short chain nitrocompounds as a treatment of layer hen manure and litter; effects on in vitro survivability of Salmonella, generic E. coli and nitrogen metabolism. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2017; 52:23-29. [PMID: 27628961 DOI: 10.1080/03601234.2016.1224698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The current study was conducted to assess the bactericidal effectiveness of several nitrocompounds against pathogens in layer hen manure and litter. Evidence from an initial study indicated that treatment of layer hen manure with 12 mM nitroethane decreased populations of generic E. coli and total coliforms by 0.7 and 2.2 log10 colony forming units (CFU) g-1, respectively, after 24 h aerobic incubation at ambient temperature when compared to untreated populations. Salmonella concentrations were unaffected by nitroethane in this study. In a follow-up experiment, treatment of 6-month-old layer hen litter (mixed with 0.4 mL water g-1) with 44 mM 2-nitroethanol, 2-nitropropanol or ethyl nitroacetate decreased an inoculated Salmonella typhimurium strain from its initial concentration (3 log10 CFU g-1) by 0.7 to 1.7 log10 CFU g-1 after 6 h incubation at 37°C in covered containers. After 24 h incubation, populations of the inoculated S. Typhmiurium in litter treated with 44 mM 2-nitroethanol, 2-nitropropanol, ethyl nitroacetate or nitroethane were decreased more than 3.2 log10 CFU g-1 compared to populations in untreated control litter. Treatment of litter with 44 mM 2-nitroethanol, 2-nitropropanol, ethyl nitroacetate decreased rates of ammonia accumulation more than 70% compared to untreated controls (0.167 µmol mL-1 h-1) and loses of uric acid (< 1 µmol mL-1) were observed only in litter treated with 44 mM 2-nitropropanol, indicating that some of these nitrocompounds may help prevent loss of nitrogen in treated litter. Results warrant further research to determine if these nitrocompounds can be developed into an environmentally sustainable and safe strategy to eliminate pathogens from poultry litter, while preserving its nitrogen content as a nutritionally valuable crude protein source for ruminants.
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Becker T, Pasteels J, Weigel C, Dahse HM, Voigt K, Boland W. A tale of four kingdoms – isoxazolin-5-one- and 3-nitropropanoic acid-derived natural products. Nat Prod Rep 2017; 34:343-360. [DOI: 10.1039/c6np00122j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The occurrence, structural diversity, (bio-)synthesis, properties and detoxification mechanisms of isoxazolinone- and 3-nitropropanoic acid-derived natural compounds are reviewed.
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Affiliation(s)
- Tobias Becker
- Department of Bioorganic Chemistry
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
| | - Jacques Pasteels
- Department of Biology
- Université Libre de Bruxelles
- Brussels
- Belgium
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans Knoell Institute
- Jena
- Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
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Zhang Y, Long R, Anderson RC, Hume ME, Coverdale JA, Latham EA, Nisbet DJ. Characterization of Nitrate-Reducing and Amino Acid–Using Bacteria Prominent in Nitrotoxin-Enriched Equine Cecal Populations. J Equine Vet Sci 2016. [DOI: 10.1016/j.jevs.2016.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Anderson RC, Ripley LH, Bowman JGP, Callaway TR, Genovese KJ, Beier RC, Harvey RB, Nisbet DJ. Ruminal Fermentation of Anti-Methanogenic Nitrate- and Nitro-Containing Forages In Vitro. Front Vet Sci 2016; 3:62. [PMID: 27563646 PMCID: PMC4980585 DOI: 10.3389/fvets.2016.00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/28/2016] [Indexed: 11/20/2022] Open
Abstract
Nitrate, 3-nitro-1-propionic acid (NPA) and 3-nitro-1-propanol (NPOH) can accumulate in forages and be poisonous to animals if consumed in high enough amounts. These chemicals are also recognized as potent anti-methanogenic compounds, but plants naturally containing these chemicals have been studied little in this regard. Presently, we found that nitrate-, NPA-, or NPOH-containing forages effectively decreased methane production, by 35–87%, during in vitro fermentation by mixed cultures of ruminal microbes compared to fermentation by cultures incubated similarly with alfalfa. Methane production was further decreased during the incubation of mixed cultures also inoculated with Denitrobacterium detoxificans, a ruminal bacterium known to metabolize nitrate, NPA, and NPOH. Inhibition of methanogens within the mixed cultures was greatest with the NPA- and NPOH-containing forages. Hydrogen accumulated in all the mixed cultures incubated with forages containing nitrate, NPA or NPOH and was dramatically higher, exceeding 40 μmol hydrogen/mL, in mixed cultures incubated with NPA-containing forage but not inoculated with D. detoxificans. This possibly reflects the inhibition of hydrogenase-catalyzed uptake of hydrogen produced via conversion of 50 μmol added formate per milliliter to hydrogen. Accumulations of volatile fatty acids revealed compensatory changes in fermentation in mixed cultures incubated with the nitrate-, NPA-, and NPOH-containing forages as evidenced by lower accumulations of acetate, and in some cases, higher accumulations of butyrate and lower accumulations of ammonia, iso-buytrate, and iso-valerate compared to cultures incubated with alfalfa. Results reveal that nitrate, NPA, and NPOH that accumulate naturally in forages can be made available within ruminal incubations to inhibit methanogenesis. Further research is warranted to determine if diets can be formulated with nitrate-, NPA-, and NPOH-containing forages to achieve efficacious mitigation in ruminant methane emissions without adversely affecting fermentative efficiency or risking toxicity to animals.
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Affiliation(s)
- Robin C Anderson
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - Laura H Ripley
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - Jan G P Bowman
- Department of Animal and Range Sciences, Montana State University , Bozeman, MT , USA
| | - Todd R Callaway
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - Kenneth J Genovese
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - Ross C Beier
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - Roger B Harvey
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
| | - David J Nisbet
- Food and Feed Safety Research Unit, United States Department of Agriculture Agricultural Research Service , College Station, TX , USA
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Copado R, Arzola C, Epps SVR, Rodriguez-Almeida F, Ruiz O, Rodriguez-Muela C, Castillo YC, Corral-Luna A, Salinas J. Effect of repeated suboptimal chlorate treatment on ruminal and fecal bacterial diversity. J Food Prot 2014; 77:1588-92. [PMID: 25198852 DOI: 10.4315/0362-028x.jfp-14-140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The minimal effective dose of sodium chlorate as an intervention to reduce the carriage of pathogenic bacteria in food-producing animals has not been clearly established. The effect of low-level oral chlorate administration to ewes was assessed by comparing the diversity of prominent bacterial populations in their gastrointestinal tract. Twelve lactating crossed Pelibuey and Blackbelly-Dorper ewes (average body weight, 65 kg) were randomly assigned (four per treatment) to receive a control treatment (TC; consisting of 3 g of NaCl per animal per day) or one of two chlorate treatments (T3 or T9; consisting of 1.8 or 5.4 g of NaClO3 per animal per day, respectively). Treatments were administered twice daily via oral gavage for 5 days. Ruminal and fecal samples were collected daily, starting 3 days before and ending 6 days after treatment, and were subjected to denaturing gradient gel electrophoresis of the 16S rRNA gene sequence amplified from total population DNA. For ruminal microbes, percent similarity coefficients (SCs) between groups varied from 23.0 to 67.5% and from 39.4 to 43.3% during pretreatment and treatment periods, respectively. During the treatment period, SCs within groups ranged from 39.4 to 90.3%, 43.3 to 86.7%, and 67.5 to 92.4% for TC, T3, and T9, respectively. For fecal microbes, SCs between groups varied from 38.0 to 85.2% and 38.0 to 94.2% during pretreatment and treatment periods, respectively. SCs for fecal populations during treatment were most varied for TC (38.0 to 67.9%), intermediate for T9 (75.6 to 92.0%), and least varied for T3 (80.6 to 90.6%). Heterogeneity within and between groups provided no evidence of an effect of chlorate treatment on ruminal or fecal microbial populations.
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Affiliation(s)
- R Copado
- Autonomous University of Nuevo Leon, Monterrey, Nuevo Leon 66451, Mexico
| | - C Arzola
- Autonomous University of Chihuahua, Chihuahua 31203, Mexico.
| | - S V R Epps
- Department of Veterinary Integrative Bioscience, Texas A&M University, College Station, Texas 77843, USA
| | | | - O Ruiz
- Autonomous University of Chihuahua, Chihuahua 31203, Mexico
| | | | | | | | - J Salinas
- Autonomous University of Tamaulipas, Ciudad Victoria, Tamaulipas 87000, Mexico
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Zhang D, Zhang C, Li Z, Suzuki D, Komatsu DD, Tsunogai U, Katayama A. Electrochemical stimulation of microbial reductive dechlorination of pentachlorophenol using solid-state redox mediator (humin) immobilization. BIORESOURCE TECHNOLOGY 2014; 164:232-240. [PMID: 24859215 DOI: 10.1016/j.biortech.2014.04.071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/13/2014] [Accepted: 04/21/2014] [Indexed: 06/03/2023]
Abstract
Immobilized solid-phase humin on a graphite electrode set at -500 mV (vs. standard hydrogen electrode) significantly enhanced the microbial reductive dechlorination of pentachlorophenol as a stable solid-phase redox mediator in bioelectrochemical systems (BESs). Compared with the suspended system, the immobilized system dechlorinated PCP at a much higher efficiency, achieving 116 μmol Cl(-)g(-1) humin d(-1). Fluorescence microscopy showed a conspicuous growth of bacteria on the negatively poised immobilized humin. Electron balance analyses suggested that the electrons required for microbial dechlorination were supplied primarily from the humin-immobilized electrode. Microbial community analyses based on 16S rRNA genes showed that Dehalobacter and Desulfovibrio grew on the immobilized humin as potential dechlorinators. These findings extend the potential of BESs using immobilized solid-phase humin as the redox mediator for in situ bioremediation, given the wide distribution of humin and its efficiency and stability as a mediator.
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Affiliation(s)
- Dongdong Zhang
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Chunfang Zhang
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Zhiling Li
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Daisuke Suzuki
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Daisuke D Komatsu
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Arata Katayama
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan; EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan.
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Noguchi M, Kurisu F, Kasuga I, Furumai H. Time-resolved DNA stable isotope probing links Desulfobacterales- and Coriobacteriaceae-related bacteria to anaerobic degradation of benzene under methanogenic conditions. Microbes Environ 2014; 29:191-9. [PMID: 24909708 PMCID: PMC4103526 DOI: 10.1264/jsme2.me13104] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
To identify the microorganisms involved in benzene degradation, DNA-stable isotope probing (SIP) with 13C-benzene was applied to a methanogenic benzene-degrading enrichment culture. Pyrosequencing of ribosomal RNA (rRNA) gene sequences revealed that the community structure was highly complex in spite of a 3-year incubation only with benzene. The culture degraded 98% of approximately 1 mM 13C-benzene and mineralized 72% of that within 63 d. The terminal restriction fragment length polymorphism (T-RFLP) profiles of the buoyant density fractions revealed the incorporation of 13C into two phylotypes after 64 d. These two phylotypes were determined to be Desulfobacterales- and Coriobacteriaceae-related bacteria by cloning and sequencing of the 16S rRNA gene in the 13C-labeled DNA abundant fraction. Comparative pyrosequencing analysis of the buoyant density fractions of 12C- and 13C-labeled samples indicated the incorporation of 13C into three bacterial and one archaeal OTUs related to Desulfobacterales, Coriobacteriales, Rhodocyclaceae, and Methanosarcinales. The first two OTUs included the bacteria detected by T-RFLP-cloning-sequencing analysis. Furthermore, time-resolved SIP analysis confirmed that the activity of all these microbes appeared at the earliest stage of degradation. In this methanogenic culture, Desulfobacterales- and Coriobacteriaceae-related bacteria were most likely to be the major benzene degraders.
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Affiliation(s)
- Mana Noguchi
- Research Center for Water Environment Technology, The University of Tokyo
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Ramasamy D, Dubourg G, Robert C, Caputo A, Papazian L, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov. Stand Genomic Sci 2014; 9:970-86. [PMID: 25197477 PMCID: PMC4149031 DOI: 10.4056/sigs.4878632] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enorma timonensis strain GD5(T) sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Dhamodaran Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Laurent Papazian
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Service de Réanimation Médicale, Hôpital Nord, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Correspondence: Pierre-Edouard Fournier ( )
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Characterization of bovine ruminal and equine cecal microbial populations enriched for enhanced nitro-toxin metabolizing activity. Anaerobe 2014; 26:7-13. [PMID: 24374155 DOI: 10.1016/j.anaerobe.2013.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/12/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022]
Abstract
The nitrotoxins 3-nitro-1-propionic acid (NPA) and 3-nitro-1-propanol (NPOH) are produced by a wide variety of leguminous plants, including over 150 different species and varieties of Astragalus potentially grazed by livestock. These toxins are known to be detoxified by at least one ruminal bacterium but detoxification by bacteria from other gut habitats is not known. In the present study, mixed populations of bovine ruminal and equine cecal microbes were enriched for NPA-metabolizing bacteria via consecutive 24-72 h culture in a basal minimal rumen fluid-based medium supplemented with 4.2 mM NPA and H₂ as the energy source. Rates of NPA metabolism by the respective populations increased from 58.4 ± 4.8 and 8.6 ± 11.6 nmol NPA/mL per h during initial culture to 88.9 ± 30.6 and 50.2 ± 30.9 nmol NPA/mL per h following enrichment. Results from 3-tube most probable number tests indicated that numbers of NPA-degrading microbes increased 2.1 and 1.8 log₁₀ units during enrichment from numbers measured pre-enrichment (3.9 × 10³ and 4.3 × 10¹ cells/mL for ruminal and equine cecal populations, respectively). Hydrogen, formate, and to a lesser extent, DL-lactic acid, served as electron donors to the enriched populations and CO₂ or formate were needed to maintain high rates of NPA-metabolism. The NPA-enriched populations were able to metabolize nitrate which, being a preferred electron acceptor, was antagonistic to NPA metabolism. Supplemental NPA was inhibitory to methanogenesis. Fermentation balance estimates indicated that only 47.6% of carbon available in potential substrates was recovered in headspace CO₂, volatile fatty acids or unmetabolized NPA after 72 h incubation of NPA-enriched populations that had metabolized 98% of 8.4 mM added NPA. Overall, these results reveal low level carriage of NPA-metabolizing, CO₂ or formate-requiring bacterial populations in the equine cecum yet support the concept that Denitrobacterium detoxificans-like organisms may well be the functional agents of NPA and NPOH detoxification in the populations studied here.
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Mishra AK, Hugon P, Lagier JC, Nguyen TT, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae. Stand Genomic Sci 2013; 8:290-305. [PMID: 23991260 PMCID: PMC3746427 DOI: 10.4056/sigs.3426906] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Enorma massiliensis strain phI(T) is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phI(T) is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes.
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Mao S, Huo W, Zhu W. Use of Pyrosequencing to Characterize the Microbiota in the Ileum of Goats Fed with Increasing Proportion of Dietary Grain. Curr Microbiol 2013; 67:341-50. [DOI: 10.1007/s00284-013-0371-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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Gupta RS, Chen WJ, Adeolu M, Chai Y. Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int J Syst Evol Microbiol 2013; 63:3379-3397. [PMID: 23524353 DOI: 10.1099/ijs.0.048371-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species of the class Coriobacteriia are currently distinguished from other bacteria primarily on the basis of their branching in the 16S rRNA gene trees. No reliable molecular marker is known that distinguishes the bacteria of this class from other organisms. We report here the results of detailed phylogenetic and comparative analyses on 22 sequenced genomes from members of the class Coriobacteriia. Detailed comparative analyses on protein sequences from these genomes, reported here, have identified 66 conserved signature inserts or deletions (i.e. indels) (CSIs) in widely distributed proteins that are specific for a number of different clades of the class Coriobacteriia at multiple phylogenetic levels, which are also supported by phylogenetic analyses. A set of 24 CSIs in different proteins are specific for all sequenced members of the class Coriobacteriia, providing novel molecular markers distinguishing and delimiting this class. One additional CSI is uniquely present in all members of the class Coriobacteriia and the phylum Actinobacteria supporting their placement within this bacterial phylum. A set of 16 CSIs in divergent proteins are uniquely found in the genomes of all species for which sequences are available from the glucose-fermenting genera Coriobacterium, Collinsella, Atopobium and Olsenella, but they are not present in any other bacteria. The species from these genera also form a strongly supported clade (Clade I) in the phylogenetic trees based upon concatenated protein sequences and the 16S rRNA. An additional 10 CSIs in different proteins are specifically present in all members of the asaccharolytic genera Eggerthella, Cryptobacterium, Slackia and Gordonibacter for which sequence data is available. A clade consisting of these genera (Clade II) is also supported by our phylogenetic analyses. Within Clade I, two smaller clades, one consisting of the genera Coriobacterium and Collinsella and the other containing the genera Atopobium and Olsenella, are independently supported by multiple CSIs (eight and seven respectively) and our phylogenetic analyses. Based upon the results of phylogenetic studies and the identified molecular markers, which clearly distinguish and demarcate the above indicated clades of the class Coriobacteriia at different phylogenetic depths, we propose division of the class Coriobacteriia into two orders (viz. Coriobacteriales and Eggerthellales ord. nov.) and three families (viz. Coriobacteriaceae, Atopobiaceae fam. nov. and Eggerthellaceae fam. nov.). Additionally, descriptions of the class Coriobacteriia, the order Coriobacteriales and the family Coriobacteriaceea are also emended.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Wan Jun Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Yujuan Chai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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Lagier JC, Elkarkouri K, Rivet R, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci 2013; 7:343-56. [PMID: 24019984 PMCID: PMC3764928 DOI: 10.4056/sigs.3246665] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Senegalemassilia anaerobia strain JC110(T) sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes.
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Affiliation(s)
| | - Khalid Elkarkouri
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Romain Rivet
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Carine Couderc
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
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Variability of Actinobacteria, a minor component of rumen microflora. Folia Microbiol (Praha) 2012; 57:351-3. [PMID: 22528311 DOI: 10.1007/s12223-012-0140-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/04/2012] [Indexed: 10/28/2022]
Abstract
Actinobacteria (Actinomycetes) are a significant and interesting group of gram-positive bacteria. They are regular, though infrequent, members of the microbial life in the rumen and represent up to 3 % of total rumen bacteria; there is considerable lack of information about ecology and biology of rumen actinobacteria. During the characterization of variability of rumen treponemas using non-cultivation approach, we also noted the variability of rumen actinobacteria. By using Treponema-specific primers a specific 16S rRNA gene library was prepared from cow and sheep rumen total DNA. About 10 % of recombinant clones contained actinobacteria-like sequences. Phylogenetic analyses of 11 clones obtained showed the high variability of actinobacteria in the ruminant digestive system. While some sequences are nearly identical to known sequences of actinobacteria, we detected completely new clusters of actinobacteria-like sequences, representing probably new, as yet undiscovered, group of rumen Actinobacteria. Further research will be necessary for understanding their nature and functions in the rumen.
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Brown EG, Anderson RC, Carstens GE, Gutierrez-Bañuelos H, McReynolds JL, Slay LJ, Callaway TR, Nisbet DJ. Effects of oral nitroethane administration on enteric methane emissions and ruminal fermentation in cattle. Anim Feed Sci Technol 2011. [DOI: 10.1016/j.anifeedsci.2011.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 2011; 6:e17000. [PMID: 21359220 PMCID: PMC3040199 DOI: 10.1371/journal.pone.0017000] [Citation(s) in RCA: 393] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 01/18/2011] [Indexed: 11/26/2022] Open
Abstract
Background Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. Methodology/Principal Findings We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. Conclusions/Significance Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.
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Affiliation(s)
- Heiko Nacke
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Antje Wollherr
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Christiane Will
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Ladislav Hodac
- Experimental Phycology and Culture Collection of Algae at the University of Göttingen, Göttingen, Germany
| | - Nadine Herold
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Ingo Schöning
- Institute of Ecology, Friedrich-Schiller-University, Jena, Germany
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
- * E-mail:
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Chemical inhibitors of methanogenesis and putative applications. Appl Microbiol Biotechnol 2010; 89:1333-40. [PMID: 21193988 DOI: 10.1007/s00253-010-3066-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 12/03/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
This mini-review summarizes the category, characteristics, and the application fields of the chemical methanogenic inhibitors. Usually, the chemical methanogenic inhibitors can be divided into "specific" and nonspecific inhibitors. The former group includes the structural analogs of coenzyme M and HMG-CoA inhibitors. The nonspecific group includes many chemicals which can inhibit the activity of both methanogens and non-methanogens. The chemical inhibitors of methanogenesis have been widely used in the fields of understanding methane production and consumption in pure culture or in complex natural environment, production of value-added substances, such as volatile fatty acids and hydrogen, and reduction of energy loss and improvement of the efficiency of ruminal energetic transformations. Finally, with an increasing understanding of the mechanistic effects of the chemical inhibitors of methanogenesis, it is possible that some could be used to develop into promising feed additives to reduce losses associated with enteric methane production or as useful tools to screen microbial consortia from various biotechnological applications to enhance hydrogen and acid production.
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Würdemann D, Tindall BJ, Pukall R, Lünsdorf H, Strömpl C, Namuth T, Nahrstedt H, Wos-Oxley M, Ott S, Schreiber S, Timmis KN, Oxley APA. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2009; 59:1405-15. [PMID: 19502325 DOI: 10.1099/ijs.0.005900-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-b(T), was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-b(T) (=DSM 19378(T) =CCUG 55131(T)) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10(T) (=DSM 16106(T) =CCUG 49250(T)).
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Affiliation(s)
- Dieco Würdemann
- Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
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