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Paul A. Lawson - One of the best experts on this subject based on the ideXlab platform.
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peptoniphilus stercorisuis sp nov isolated from a swine Manure Storage tank and description of peptoniphilaceae fam nov
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Crystal N Johnson, Michael A Cotta, Terence R Whitehead, Robert E Rhoades, Paul A. LawsonAbstract:A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine Manure Storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales , within the phylum Firmicutes . Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus , most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5 %. The major long-chain fatty acids were found to be C14 : 0 (22.4 %), C16 : 0 (15.6 %), C16 : 1ω7c (11.3 %) and C16 : 0 ALDE (10.1 %) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1T ( = DSM 27563T = NBRC 109839T). In addition, it is proposed to accommodate the genera Peptoniphilus , Anaerococcus , Anaerosphaera , Finegoldia , Gallicola , Helcococcus , Murdochiella and Parvimonas in a new family of the order Clostridiales , for which the name Peptoniphilaceae fam. nov. is proposed; the type genus of the family is Peptoniphilus .
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Two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine-Manure Storage pit
Antonie van Leeuwenhoek, 2013Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-Manure Storage pit. On the basis of the 16S rRNA, RNA polymerase α-subunit ( rpo A) and 60 kDa chaperonin ( cpn60 ) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C_16:0, C_16:1 ω7c, C_16:1 ω7c, and C_18:1 ω7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32^T = CCUG 61260^T = NRRL B-59661^T) and Enterococcus eurekensis sp. nov. (type strain PC4B^T = CCUG 61259^T = NRRL B-59662^T) are proposed for these hitherto undescribed species.
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peptostreptococcus russellii sp nov isolated from a swine Manure Storage pit
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Terence R Whitehead, Edward R B Moore, Michael A Cotta, Enevold Falsen, Paul A. LawsonAbstract:Using a polyphasic approach, a taxonomic study was performed on seven strains of an unknown Gram-reaction-positive, non-spore-forming, obligately anaerobic coccus-shaped bacterium, isolated from a swine-Manure Storage pit. Comparative 16S rRNA gene sequencing confirmed that all seven isolates were highly related to each other and formed a hitherto unknown lineage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism was most closely related to Peptostreptococcus anaerobius CCUG 7835T and Peptostreptococcus stomatis CCUG 51858T with 16S rRNA gene sequence similarities of 95.5 and 93.0 %, respectively. The peptidoglycan type of the cell wall was determined to be A4α l-Lys–d-Asp and glucose, xylose and traces of mannose were detected as the cell–wall sugars. Based on biochemical, chemotaxonomic and phylogenetic evidence the unknown bacterium represents a new species of the genus Peptostreptococcus, for which the name Peptostreptococcus russellii sp. nov, is proposed. The type strain is RT-10BT ( = CCUG 58235T = NRRL B-59380T = DSM 23041T).
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Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-Manure Storage pit and a human clinical source.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-Manure Storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the Manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).
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Vagococcus elongatus sp. nov., isolated from a swine-Manure Storage pit.
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Paul A. Lawson, Michael A Cotta, Enevold Falsen, Terence R WhiteheadAbstract:A polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-Manure Storage pit. The bacterium, designated strain PPC9(T), was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9(T) was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9(T) is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9(T) (=CCUG 51432(T)=NRRL B-41357(T)).
Terence R Whitehead - One of the best experts on this subject based on the ideXlab platform.
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Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit
Genome announcements, 2016Co-Authors: Bradd J. Haley, Seon Woo Kim, Terence R WhiteheadAbstract:ABSTRACT The swine gastrointestinal tract and stored swine Manure may serve as reservoirs of antibiotic resistance genes, as well as sources of novel bacteria. Here, we report the draft genome sequence of a novel taxon in the Erysipelotrichaceae family, isolated from a swine Manure Storage pit that is resistant to multiple antibiotics.
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peptoniphilus stercorisuis sp nov isolated from a swine Manure Storage tank and description of peptoniphilaceae fam nov
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Crystal N Johnson, Michael A Cotta, Terence R Whitehead, Robert E Rhoades, Paul A. LawsonAbstract:A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine Manure Storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales , within the phylum Firmicutes . Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus , most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5 %. The major long-chain fatty acids were found to be C14 : 0 (22.4 %), C16 : 0 (15.6 %), C16 : 1ω7c (11.3 %) and C16 : 0 ALDE (10.1 %) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1T ( = DSM 27563T = NBRC 109839T). In addition, it is proposed to accommodate the genera Peptoniphilus , Anaerococcus , Anaerosphaera , Finegoldia , Gallicola , Helcococcus , Murdochiella and Parvimonas in a new family of the order Clostridiales , for which the name Peptoniphilaceae fam. nov. is proposed; the type genus of the family is Peptoniphilus .
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Two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine-Manure Storage pit
Antonie van Leeuwenhoek, 2013Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-Manure Storage pit. On the basis of the 16S rRNA, RNA polymerase α-subunit ( rpo A) and 60 kDa chaperonin ( cpn60 ) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C_16:0, C_16:1 ω7c, C_16:1 ω7c, and C_18:1 ω7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32^T = CCUG 61260^T = NRRL B-59661^T) and Enterococcus eurekensis sp. nov. (type strain PC4B^T = CCUG 61259^T = NRRL B-59662^T) are proposed for these hitherto undescribed species.
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peptostreptococcus russellii sp nov isolated from a swine Manure Storage pit
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Terence R Whitehead, Edward R B Moore, Michael A Cotta, Enevold Falsen, Paul A. LawsonAbstract:Using a polyphasic approach, a taxonomic study was performed on seven strains of an unknown Gram-reaction-positive, non-spore-forming, obligately anaerobic coccus-shaped bacterium, isolated from a swine-Manure Storage pit. Comparative 16S rRNA gene sequencing confirmed that all seven isolates were highly related to each other and formed a hitherto unknown lineage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism was most closely related to Peptostreptococcus anaerobius CCUG 7835T and Peptostreptococcus stomatis CCUG 51858T with 16S rRNA gene sequence similarities of 95.5 and 93.0 %, respectively. The peptidoglycan type of the cell wall was determined to be A4α l-Lys–d-Asp and glucose, xylose and traces of mannose were detected as the cell–wall sugars. Based on biochemical, chemotaxonomic and phylogenetic evidence the unknown bacterium represents a new species of the genus Peptostreptococcus, for which the name Peptostreptococcus russellii sp. nov, is proposed. The type strain is RT-10BT ( = CCUG 58235T = NRRL B-59380T = DSM 23041T).
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Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-Manure Storage pit and a human clinical source.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-Manure Storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the Manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).
Michael A Cotta - One of the best experts on this subject based on the ideXlab platform.
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peptoniphilus stercorisuis sp nov isolated from a swine Manure Storage tank and description of peptoniphilaceae fam nov
International Journal of Systematic and Evolutionary Microbiology, 2014Co-Authors: Crystal N Johnson, Michael A Cotta, Terence R Whitehead, Robert E Rhoades, Paul A. LawsonAbstract:A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine Manure Storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales , within the phylum Firmicutes . Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus , most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5 %. The major long-chain fatty acids were found to be C14 : 0 (22.4 %), C16 : 0 (15.6 %), C16 : 1ω7c (11.3 %) and C16 : 0 ALDE (10.1 %) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1T ( = DSM 27563T = NBRC 109839T). In addition, it is proposed to accommodate the genera Peptoniphilus , Anaerococcus , Anaerosphaera , Finegoldia , Gallicola , Helcococcus , Murdochiella and Parvimonas in a new family of the order Clostridiales , for which the name Peptoniphilaceae fam. nov. is proposed; the type genus of the family is Peptoniphilus .
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Two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine-Manure Storage pit
Antonie van Leeuwenhoek, 2013Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-Manure Storage pit. On the basis of the 16S rRNA, RNA polymerase α-subunit ( rpo A) and 60 kDa chaperonin ( cpn60 ) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C_16:0, C_16:1 ω7c, C_16:1 ω7c, and C_18:1 ω7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32^T = CCUG 61260^T = NRRL B-59661^T) and Enterococcus eurekensis sp. nov. (type strain PC4B^T = CCUG 61259^T = NRRL B-59662^T) are proposed for these hitherto undescribed species.
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peptostreptococcus russellii sp nov isolated from a swine Manure Storage pit
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Terence R Whitehead, Edward R B Moore, Michael A Cotta, Enevold Falsen, Paul A. LawsonAbstract:Using a polyphasic approach, a taxonomic study was performed on seven strains of an unknown Gram-reaction-positive, non-spore-forming, obligately anaerobic coccus-shaped bacterium, isolated from a swine-Manure Storage pit. Comparative 16S rRNA gene sequencing confirmed that all seven isolates were highly related to each other and formed a hitherto unknown lineage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism was most closely related to Peptostreptococcus anaerobius CCUG 7835T and Peptostreptococcus stomatis CCUG 51858T with 16S rRNA gene sequence similarities of 95.5 and 93.0 %, respectively. The peptidoglycan type of the cell wall was determined to be A4α l-Lys–d-Asp and glucose, xylose and traces of mannose were detected as the cell–wall sugars. Based on biochemical, chemotaxonomic and phylogenetic evidence the unknown bacterium represents a new species of the genus Peptostreptococcus, for which the name Peptostreptococcus russellii sp. nov, is proposed. The type strain is RT-10BT ( = CCUG 58235T = NRRL B-59380T = DSM 23041T).
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Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-Manure Storage pit and a human clinical source.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: Michael A Cotta, Terence R Whitehead, Enevold Falsen, Edward Moore, Paul A. LawsonAbstract:A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-Manure Storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the Manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).
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Vagococcus elongatus sp. nov., isolated from a swine-Manure Storage pit.
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Paul A. Lawson, Michael A Cotta, Enevold Falsen, Terence R WhiteheadAbstract:A polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-Manure Storage pit. The bacterium, designated strain PPC9(T), was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9(T) was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9(T) is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9(T) (=CCUG 51432(T)=NRRL B-41357(T)).
Edward Topp - One of the best experts on this subject based on the ideXlab platform.
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Physico-chemical characteristics and methanogen communities in swine and dairy Manure Storage tanks: Spatio-temporal variations and impact on methanogenic activity
Water Research, 2013Co-Authors: Maialen Barret, Lucie Masse, Edward Topp, Daniel I Masse, Nathalie Gagnon, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major environmental problem associated with the management of Manure from the livestock industry. Methane is the primary GHG emitted during Manure outdoor Storage. In this paper, the variability of two swine and two dairy Manure Storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of Manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of Manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in Storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy Manure Storage tanks.
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identification of methanoculleus spp as active methanogens during anoxic incubations of swine Manure Storage tank samples
Applied and Environmental Microbiology, 2013Co-Authors: Maialen Barret, Martin Kalmokoff, Stephen P. J. Brooks, Yris Verastegui, Fernando Matias, Josh D. Neufeld, Edward Topp, Nathalie Gagnon, Guylaine TalbotAbstract:Methane emissions represent a major environmental concern associated with Manure management in the livestock industry. A more thorough understanding of how microbial communities function in Manure Storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine Manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of Manure samples under anoxic conditions to induce substrate starvation, [U-¹³C] acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (~7g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine Manure Storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.
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methanoculleus spp as a biomarker of methanogenic activity in swine Manure Storage tanks
FEMS Microbiology Ecology, 2012Co-Authors: Maialen Barret, Lucie Masse, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Edward Topp, Daniel I Masse, Nathalie Gagnon, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major problem associated with Manure management in the livestock industry. A prerequisite to mitigate methane emissions occurring during Manure Storage is a clearer understanding of how the microbial consortia involved in methanogenesis function. Here, we have examined Manure stored in outdoor tanks from two different farms, at different locations and depths. Physico-chemical and microbiological characterization of these samples indicated differences between each tank, as well as differences within each tank dependent on the depth of sampling. The dynamics of both the bacterial and archaeal communities within these samples were monitored over a 150-day period of anaerobic incubation to identify and track emerging microorganisms, which may be temporally important in the methanogenesis process. Analyses based on DNA fingerprinting of microbial communities identified trends common among all samples as well as trends specific to certain samples. All archaeal communities became enriched with Methanoculleus spp. over time, indicating that the hydrogenotrophic pathway of methanogenesis predominated. Although the emerging species differed in samples obtained from shallow depths compared to deep samples, the temporal enrichment of Methanoculleus suggests that this genus may represent a relevant indicator of methanogenic activity in swine Manure Storage tanks.
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Dynamics of antimicrobial resistance and virulence genes in Enterococcus faecalis during swine Manure Storage
Canadian journal of microbiology, 2010Co-Authors: Anil Mangalappalli-illathua. Mangalappalli-illathu, Patrick Duriez, Luke Masson, Moussa Sory Diarra, Andrew Scotta. Scott, Yuan-ching Tieny.-c. Tien, Yun Zhangy. Zhang, Edward ToppAbstract:In this study we used 2 experimental approaches to evaluate the stability of antimicrobial resistance (AMR) phe- notypes, selected AMR genes, and selected virulence genes in Enterococcus faecalis during Manure Storage on a commer- cial swine farm. Isolates of E. faecalis were obtained directly from fresh fecal material (n = 120) and from the Manure Storage facility (n = 85) and compared. Tetracycline resistance and the virulence genes cob, esp, eep, and ccf were de- tected at lower frequency in Manure isolates than in fecal isolates. A second approach consisted of immersing in diffusion chambers pure cultures of E. faecalis that varied in their AMR phenotypes and virulence genotypes in the swine Manure Storage facility for 8 weeks, sampling periodically, and evaluating the recovered strains for changes in their genotypic or phenotypic characteristics. Enterococcus faecalis populations declined exponentially, with rate constants ranging from 0.011 to 0.022 h -1 . Among the AMR and virulence genes examined, 1 AMR gene (sat4) and 7 virulence genes (agrBfs, cob, cpd, cylB, efaAfs, enlA, and esp) were lost at low frequencies in the recovered strains. The AMR phenotypes were sta- ble during the incubation, with minimal loss (P > 0.05) of the streptomycin-resistance phenotype. Overall, these results suggest that some attributes of public health significance in populations of E. faecalis decrease in frequency during Manure Storage.
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Loss of virulence genes in Escherichia coli populations during Manure Storage on a commercial swine farm.
Applied and environmental microbiology, 2008Co-Authors: Patrick Duriez, Yun Zhang, Andrew Scott, Edward ToppAbstract:Confined livestock production farms typically store their wastes prior to land application. Here, we employed three complementary approaches to evaluate changes in the population structure and stability of virulence genes in Escherichia coli during Manure Storage on a commercial farm that housed healthy swine. Isolates were genotyped by repetitive extragenic palindromic PCR using the BOXA1R primer and evaluated for the presence of selected virulence genes by PCR. Isolates obtained from the Manure holding tank (n = 392) carried estB, fedA, stx(2e), astA, paa, aida-I, and sepA at lower frequencies than isolates obtained from fresh feces (n = 412). Fresh fecal material from the barn was added into diffusion chambers and immersed in the Manure holding tank for 7 weeks. The fecal E. coli population was initially dominated by a single genotype, all isolates of which carried fedA and aida-I. After 7 weeks, a genotype that did not carry any virulence genes dominated the surviving population. In a second experiment, 48 fecal isolates of E. coli that varied in their genotypes and virulence gene complement were incubated in diffusion chambers in the Manure holding tank for 3 weeks. Over 95% of the inoculum population carried at least one virulence gene, whereas after 3 weeks 90% of the recovered isolates carried no virulence genes. Taken together, these results indicate that during commercial Manure Storage, there was a significant reduction in the carriage of these virulence genes by E. coli. We propose that loss of virulence genes from enteric pathogens in the farm and in natural environments may, if generalized, contribute to the attenuation of a public health risk from contamination with agricultural wastes.
Guylaine Talbot - One of the best experts on this subject based on the ideXlab platform.
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Physico-chemical characteristics and methanogen communities in swine and dairy Manure Storage tanks: Spatio-temporal variations and impact on methanogenic activity
Water Research, 2013Co-Authors: Maialen Barret, Lucie Masse, Edward Topp, Daniel I Masse, Nathalie Gagnon, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major environmental problem associated with the management of Manure from the livestock industry. Methane is the primary GHG emitted during Manure outdoor Storage. In this paper, the variability of two swine and two dairy Manure Storage tanks was surveyed, in terms of physico-chemical and microbiological parameters. The impact of the inter-tank and spatio-temporal variations of these parameters on the methanogenic activity of Manure was ascertained. A Partial Least Square regression was carried out, which demonstrated that physico-chemical as well as microbiological parameters had a major influence on the methanogenic activity. Among the 19 parameters included in the regression, the concentrations of VFAs had the strongest negative influence on the methane emission rate of Manure, resulting from their well-known inhibitory effect. The relative abundance of two amplicons in archaeal fingerprints was found to positively influence the methanogenic activity, suggesting that Methanoculleus spp. and possibly Methanosarcina spp. are major contributors to methanogenesis in Storage tanks. This work gave insights into the mechanisms, which drive methanogenesis in swine and dairy Manure Storage tanks.
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identification of methanoculleus spp as active methanogens during anoxic incubations of swine Manure Storage tank samples
Applied and Environmental Microbiology, 2013Co-Authors: Maialen Barret, Martin Kalmokoff, Stephen P. J. Brooks, Yris Verastegui, Fernando Matias, Josh D. Neufeld, Edward Topp, Nathalie Gagnon, Guylaine TalbotAbstract:Methane emissions represent a major environmental concern associated with Manure management in the livestock industry. A more thorough understanding of how microbial communities function in Manure Storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine Manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of Manure samples under anoxic conditions to induce substrate starvation, [U-¹³C] acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (~7g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine Manure Storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.
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methanoculleus spp as a biomarker of methanogenic activity in swine Manure Storage tanks
FEMS Microbiology Ecology, 2012Co-Authors: Maialen Barret, Lucie Masse, Bruno Morissette, Martin Kalmokoff, Stephen P. J. Brooks, Fernando Matias, Edward Topp, Daniel I Masse, Nathalie Gagnon, Guylaine TalbotAbstract:Greenhouse gas emissions represent a major problem associated with Manure management in the livestock industry. A prerequisite to mitigate methane emissions occurring during Manure Storage is a clearer understanding of how the microbial consortia involved in methanogenesis function. Here, we have examined Manure stored in outdoor tanks from two different farms, at different locations and depths. Physico-chemical and microbiological characterization of these samples indicated differences between each tank, as well as differences within each tank dependent on the depth of sampling. The dynamics of both the bacterial and archaeal communities within these samples were monitored over a 150-day period of anaerobic incubation to identify and track emerging microorganisms, which may be temporally important in the methanogenesis process. Analyses based on DNA fingerprinting of microbial communities identified trends common among all samples as well as trends specific to certain samples. All archaeal communities became enriched with Methanoculleus spp. over time, indicating that the hydrogenotrophic pathway of methanogenesis predominated. Although the emerging species differed in samples obtained from shallow depths compared to deep samples, the temporal enrichment of Methanoculleus suggests that this genus may represent a relevant indicator of methanogenic activity in swine Manure Storage tanks.