Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR.

Abstract:

:Pollution of the environment by human and animal faecal pollution affects the safety of shellfish, drinking water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative PCR (qPCR) assays was therefore developed and applied to compare the composition of intestinal microbiota of these two groups. Primers were designed to quantify the 16S rRNA gene from dominant and subdominant bacterial groups. TaqMan probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits, goats, horses, pigs, sheep and cows. Three dominant bacterial groups (Bacteroides/Prevotella, Clostridium coccoides and Bifidobacterium) of the human microbiota showed differential population levels in animal species. The Clostridium leptum group showed the lowest differences among human and farm animal species. Human subdominant bacterial groups were highly variable in animal species. Partial least squares regression indicated that the human microbiota could be distinguished from all farm animals studied. This culture-independent comparative assessment of the faecal microbiota between humans and farm animals will prove useful in identifying biomarkers of human and animal faecal contaminations that can be applied to microbial source tracking methods.

journal_name

FEMS Microbiol Ecol

authors

Furet JP,Firmesse O,Gourmelon M,Bridonneau C,Tap J,Mondot S,Doré J,Corthier G

doi

10.1111/j.1574-6941.2009.00671.x

subject

Has Abstract

pub_date

2009-06-01 00:00:00

pages

351-62

issue

3

eissn

0168-6496

issn

1574-6941

pii

FEM671

journal_volume

68

pub_type

杂志文章
  • Estimation of long-term bacterial respiration and growth efficiency in Lake Kinneret.

    abstract::Semi-annual averaged values of photosynthetic carbon fixation (PCF), community respiration (CR), bacterial productivity (BP) and zooplankton carbon biomass, measured biweekly or monthly, were used to obtain long-term estimates of bacterial respiration (BR) and bacterial growth efficiency (BGE) in Lake Kinneret from 20...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2009.00822.x

    authors: Berman T,Yacobi YZ,Parparov A,Gal G

    更新日期:2010-03-01 00:00:00

  • Resistance and resilience of Cu-polluted soil after Cu perturbation, tested by a wide range of soil microbial parameters.

    abstract::Copper (Cu)-polluted and unpolluted soils were used to study the effect of initial pollution on soil biological resistance and resilience by measuring the responses to perturbation using different parameters. Microbial biomass carbon, substrate-induced respiration and copy numbers of 16S rRNA gene were grouped as gene...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2009.00741.x

    authors: Deng H,Li XF,Cheng WD,Zhu YG

    更新日期:2009-11-01 00:00:00

  • Antibiotic resistance patterns of Pseudomonas spp. isolated from faecal wastes in the environment and contaminated surface water.

    abstract::The Pseudomonas genus, which includes environmental and pathogenic species, is known to present antibiotic resistances, and can receive resistance genes from multi-resistant enteric bacteria released into the environment via faecal rejects. This study was aimed to investigate the resistome of Pseudomonas populations t...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa008

    authors: Camiade M,Bodilis J,Chaftar N,Riah-Anglet W,Gardères J,Buquet S,Ribeiro AF,Pawlak B

    更新日期:2020-02-01 00:00:00

  • Heterogeneity-disease relationship in the human microbiome-associated diseases.

    abstract::Space is a critical and also challenging frontier in human microbiome research. It has been found that lack of consideration of scales beyond individual and ignoring of microbe dispersal are two crucial roadblocks in preventing deep understanding of the spatial heterogeneity of human microbiome. Assessing and interpre...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa093

    authors: Ma ZS

    更新日期:2020-07-01 00:00:00

  • Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions.

    abstract::The microbial communities of in situ reactor columns degrading benzene with sulfate as an electron acceptor were analyzed based on clone libraries and terminal restriction fragment length polymorphism fingerprinting of PCR-amplified 16S rRNA genes. The columns were filled with either lava granules or sand particles an...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2008.00536.x

    authors: Kleinsteuber S,Schleinitz KM,Breitfeld J,Harms H,Richnow HH,Vogt C

    更新日期:2008-10-01 00:00:00

  • Predominance of Flavobacterium, Pseudomonas, and Polaromonas within the prokaryotic community of freshwater shallow lakes in the northern Victoria Land, East Antarctica.

    abstract::A polyphasic approach that included PCR-dependent and PCR-independent molecular techniques was applied to analyze the prokaryotic community in surface waters of shallow Antarctic lakes. The in situ abundance of different bacterial groups was determined by the fluorescence in situ hybridization, whereas bacterial diver...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2012.01394.x

    authors: Michaud L,Caruso C,Mangano S,Interdonato F,Bruni V,Lo Giudice A

    更新日期:2012-11-01 00:00:00

  • The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension.

    abstract::Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs i...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa002

    authors: Di Cesare A,Eckert EM,Cottin C,Bouchez A,Callieri C,Cortesini M,Lami A,Corno G

    更新日期:2020-02-01 00:00:00

  • Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons.

    abstract::Antimicrobial resistance is one of the most significant challenges facing the global medical community and can be attributed to the use and misuse of antibiotics. This includes use as growth promoters or for prophylaxis and treatment of bacterial infection in intensively farmed livestock from where antibiotics can ent...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiw159

    authors: Cleary DW,Bishop AH,Zhang L,Topp E,Wellington EM,Gaze WH

    更新日期:2016-10-01 00:00:00

  • Siderophore-mediated cooperation and virulence in Pseudomonas aeruginosa.

    abstract::Why should organisms cooperate with each other? Helping close relatives that are likely to share the same genes (kin selection) is one important explanation that is likely to apply across taxa. The production of metabolically costly extracellular iron-scavenging molecules (siderophores) by microorganisms is a cooperat...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1574-6941.2007.00388.x

    authors: Buckling A,Harrison F,Vos M,Brockhurst MA,Gardner A,West SA,Griffin A

    更新日期:2007-11-01 00:00:00

  • Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment.

    abstract::This study investigated the response of antibiotic resistance genes (ARGs) to nanosilver (Ag) in lab-scale nitrifying sequencing batch reactors (SBRs), compared to Ag(+)-dosed and undosed controls. Quantitative polymerase chain reaction (q-PCR) targeting sul1, tet(O), ermB and the class I integron gene intI1 and corre...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiw022

    authors: Ma Y,Metch JW,Yang Y,Pruden A,Zhang T

    更新日期:2016-03-01 00:00:00

  • On-board flow cytometric observation of picoplankton community structure in the East China Sea during the fall of different years.

    abstract::On-board flow cytometric determinations of picoplankton abundance (i.e. Synechococcus spp., Prochlorococcus spp., picoeukaryotes and also heterotrophic bacteria) were obtained in the East China Sea in fall of 2000 and 2003. The average abundances of Synechococcus, Prochlorococcus, picoeukaryotes and heterotrophic bact...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1016/j.femsec.2004.11.019

    authors: Pan LA,Zhang LH,Zhang J,Gasol JM,Chao M

    更新日期:2005-04-01 00:00:00

  • The effect of ingestion of milk supplemented with salivaricin A-producing Streptococcus salivarius on the bacteriocin-like inhibitory activity of streptococcal populations on the tongue.

    abstract::The colonization efficacies of salivaricin A (SalA)-producing Streptococcus salivarius strains 20P3 and 5 were compared when given in milk to 219 children, using either 2-day or 9-day dosing regimens. Colonization levels overall were superior for strain 5, and the 9-day dosing schedule resulted in higher levels of bot...

    journal_title:FEMS microbiology ecology

    pub_type: 临床试验,杂志文章

    doi:10.1111/j.1574-6941.2006.00228.x

    authors: Dierksen KP,Moore CJ,Inglis M,Wescombe PA,Tagg JR

    更新日期:2007-03-01 00:00:00

  • Progress towards understanding the fate of plasmids in bacterial communities.

    abstract::Plasmid-mediated horizontal gene transfer influences bacterial community structure and evolution. However, an understanding of the forces which dictate the fate of plasmids in bacterial populations remains elusive. This is in part due to the enormous diversity of plasmids, in terms of size, structure, transmission, ev...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1574-6941.2008.00505.x

    authors: Slater FR,Bailey MJ,Tett AJ,Turner SL

    更新日期:2008-10-01 00:00:00

  • Microbial dynamics in anaerobic enrichment cultures degrading di-n-butyl phthalic acid ester.

    abstract::Although anaerobic biodegradation of di-n-butyl phthalic acid ester (DBP) has been studied over the past decade, only little is known about the microorganisms involved in the biological anaerobic degradation pathways. The aim of this work is to characterize the microbial community dynamics in enrichment cultures degra...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2008.00570.x

    authors: Trably E,Batstone DJ,Christensen N,Patureau D,Schmidt JE

    更新日期:2008-11-01 00:00:00

  • Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop.

    abstract::There is interest in understanding how cultivation, plant genotype, climate and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities ca...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa145

    authors: Ramoneda J,Roux JJL,Frossard E,Frey B,Gamper HA

    更新日期:2020-10-01 00:00:00

  • Methods for field measurement of antibiotic concentrations: limitations and outlook.

    abstract::The growing prevalence of antibiotic resistance poses an increasingly serious threat to human health. Although an important driver of antibiotic resistance is the continuous exposure of bacteria to sublethal concentrations of antibiotics in natural environments, antibiotic pollutants are not currently tracked globally...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章,评审

    doi:10.1093/femsec/fiy105

    authors: Parthasarathy R,Monette CE,Bracero S,S Saha M

    更新日期:2018-08-01 00:00:00

  • Shifts in the protist community associated with an anticyclonic gyre in the Alboran Sea (Mediterranean Sea).

    abstract::The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone ...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa197

    authors: García-Gómez C,Yebra L,Cortés D,Sánchez A,Alonso A,Valcárcel-Pérez N,Gómez-Jakobsen F,Herrera I,Johnstone C,Mercado JM

    更新日期:2020-10-20 00:00:00

  • Synoptic determination of living/dead and active/dormant bacterial fractions in marine sediments.

    abstract::The most widely used methods for the estimation of the living/dead fractions of bacterial cells involve specific stains that are able to reveal membrane integrity. Here, we have compared two different probes (propidium iodide and ethidium homodimer-2) that have different molecular weights and steric hindrance effects....

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2005.00042.x

    authors: Manini E,Danovaro R

    更新日期:2006-03-01 00:00:00

  • Preferential attack of the (S)-configured ether-linked carbons in bis-(1-chloro-2-propyl) ether by Rhodococcus sp. strain DTB.

    abstract::Rhodococcus sp. strain DTB (DSM 44534) was grown on a mixture of (R,R)-, (S,S)- and meso-bis-(1-chloro-2-propyl) ether (BCPE) as the sole source of carbon and energy. During BCPE degradation 1'-chloro-2'-propyl-3-chloro-2-prop-1-enyl-ether (DVE), 1-chloro-2-propanol and chloroacetone intermediates were formed. The BCP...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2005.00004.x

    authors: Garbe LA,Moreno-Horn M,Tressl R,Görisch H

    更新日期:2006-01-01 00:00:00

  • Investigations of Rhizobium biofilm formation.

    abstract::The development of nitrogen-fixing nodules of the Rhizobium-legume symbiosis, especially the early stages of root hair deformation and curling, infection thread formation, and nodule initiation, has been well studied from a genetic standpoint. In contrast, the factors important for the colonization of surfaces by rhiz...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2005.00044.x

    authors: Fujishige NA,Kapadia NN,De Hoff PL,Hirsch AM

    更新日期:2006-05-01 00:00:00

  • Annual variation of Microcystis genotypes and their potential toxicity in water and sediment from a eutrophic reservoir.

    abstract::The relative genetic diversity of microcystin-producing Microcystis in the water and sediment of the Daechung Reservoir, Korea, was investigated over an entire year, including the cyanobacterial bloom season. The cells of potentially toxic Microcystis strains containing mcyJ genotypes and cells containing the genus-sp...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2010.00947.x

    authors: Kim SG,Joung SH,Ahn CY,Ko SR,Boo SM,Oh HM

    更新日期:2010-10-01 00:00:00

  • Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula.

    abstract::Several studies have shown that microbial communities in Antarctic environments are highly diverse. However, considering that the Antarctic Peninsula is among the regions with the fastest warming rates, and that regional climate change has been linked to an increase in the mean rate of glacier retreat, the microbial d...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiu005

    authors: Pessi IS,Osorio-Forero C,Gálvez EJ,Simões FL,Simões JC,Junca H,Macedo AJ

    更新日期:2015-01-01 00:00:00

  • Coral-associated bacterial communities on Ningaloo Reef, Western Australia.

    abstract::Coral-associated microbial communities from three coral species (Pocillopora damicornis, Acropora tenuis and Favites abdita) were examined every 3 months (January, March, June, October) over a period of 1 year on Ningaloo Reef, Western Australia. Tissue from corals was collected throughout the year and additional samp...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2010.00986.x

    authors: Ceh J,Van Keulen M,Bourne DG

    更新日期:2011-01-01 00:00:00

  • Microbiota in non-flooded and flooded rice culms.

    abstract::Rice plants are the habitat for large and diverse populations of microbes, which play important roles on rice health and productivity. However, the response of microbiome on rice culm to water flooding is poorly understood. In this study, the bacterial community on non-flooded (RSA) and flooded (RSB) rice culms was in...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiz036

    authors: Cui HL,Duan GL,Zhang H,Cheng W,Zhu YG

    更新日期:2019-04-01 00:00:00

  • Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.

    abstract::High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem serv...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa261

    authors: Metze D,Popp D,Schwab L,Keller NS,da Rocha UN,Richnow HH,Vogt C

    更新日期:2020-12-30 00:00:00

  • Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure.

    abstract::Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. ...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1093/femsec/fiaa048

    authors: Coclet C,Garnier C,Durrieu G,D'onofrio S,Layglon N,Briand JF,Misson B

    更新日期:2020-06-01 00:00:00

  • Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH.

    abstract::We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2006.00276.x

    authors: Alonso-Sáez L,Balagué V,Sà EL,Sánchez O,González JM,Pinhassi J,Massana R,Pernthaler J,Pedrós-Alió C,Gasol JM

    更新日期:2007-04-01 00:00:00

  • Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones.

    abstract::Bacillus pumilus is a Gram-positive bacterium with a wide range of attributed applications, namely as a plant growth promoting rhizobacteria (PGPR), animal, and human probiotic. However, a rare putative role in human diseases has been reported, namely in food poisoning or as anthrax-like cutaneous infectious agent. Th...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/1574-6941.12426

    authors: Branquinho R,Meirinhos-Soares L,Carriço JA,Pintado M,Peixe LV

    更新日期:2014-12-01 00:00:00

  • Effect of ammonium and acetate on methanogenic pathway and methanogenic community composition.

    abstract::Methanogenesis from acetate (aceticlastic methanogenesis or syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis) is the most important step for the biogas process. The major environmental factors influencing methanogenesis are volatile fatty acids, ammonia, pH, and temperature. In our study...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1111/j.1574-6941.2012.01456.x

    authors: Fotidis IA,Karakashev D,Kotsopoulos TA,Martzopoulos GG,Angelidaki I

    更新日期:2013-01-01 00:00:00

  • Microbial oxidation of CH(4) at different temperatures in landfill cover soils.

    abstract::Biological oxidation of CH(4) is an important constraint on the emission of this gas from areas, such as landfills to the atmosphere. We studied the effect of temperature on methanotrophic bacteria in three different landfill cover soils, incubated in the laboratory. In samples of a young cover, consisting of wood chi...

    journal_title:FEMS microbiology ecology

    pub_type: 杂志文章

    doi:10.1016/j.femsec.2004.02.006

    authors: Börjesson G,Sundh I,Svensson B

    更新日期:2004-06-01 00:00:00