How Management Practices Within a Poultry House During Successive Flock Rotations Change the Structure of the Soil Microbiome.

Abstract:

:The microbiome within a poultry production house influences the attainment of physiologically strong birds and thus food safety and public health. Yet little is known about the microbial communities within the house and the effects on the soil microbes onto which the houses are placed; nor the effects of management practices on their equilibrium. This study looked at the soil bacterial microbiome before a broiler house was constructed, then through 11 flock rotations (2.5 years) that included a partial clean-out and a total clean-out within the management regimen. Major shifts were observed, occurring at the taxonomic class level, related to the introduction of bedding and birds on top of the soil. The partial clean-out of litter did not change the soil bacterial community in any substantial way, only prompting a temporary increase in some genera; however, the total litter clean-out caused a major increase in a cohort of Actinobacteria. The underlying soil contained bacteria beneficial for poultry metabolism, such as Lactobacillus, Faecalibacterium, Bacteriodes, and Ruminococcus. Additionally, management practices affected the class structure of the soil bacterial community beneath the poultry house. The scheduling of these practices should be leveraged to exploit maintenance of beneficial bacteria that maximize microbiome contributions to bird production processes, while minimizing possible antibiotic-resistant bacteria and environmental effects.

journal_name

Front Microbiol

authors

Crippen TL,Sheffield CL,Singh B,Byrd JA,Beier RC

doi

10.3389/fmicb.2019.02100

subject

Has Abstract

pub_date

2019-09-13 00:00:00

pages

2100

issn

1664-302X

journal_volume

10

pub_type

杂志文章
  • Corrigendum: Azole-Resistance in Aspergillus terreus and Related Species: An Emerging Problem or a Rare Phenomenon?

    abstract::[This corrects the article DOI: 10.3389/fmicb.2018.00516.]. ...

    journal_title:Frontiers in microbiology

    pub_type: 已发布勘误

    doi:10.3389/fmicb.2018.03245

    authors: Zoran T,Sartori B,Sappl L,Aigner M,Sánchez-Reus F,Rezusta A,Chowdhary A,Taj-Aldeen SJ,Arendrup MC,Oliveri S,Kontoyiannis DP,Alastruey-Izquierdo A,Lagrou K,Lo Cascio G,Meis JF,Buzina W,Farina C,Drogari-Apiranthitou M,G

    更新日期:2019-01-14 00:00:00

  • Surface (S) Layer Proteins of Lactobacillus acidophilus Block Virus Infection via DC-SIGN Interaction.

    abstract::Alphaviruses and flaviviruses are important human pathogens that include Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV), which can cause diseases in humans ranging from arthralgia to hemorrhagic fevers and microcephaly. It was previously shown that treatment with surface layer (S-layer) protein,...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00810

    authors: Prado Acosta M,Geoghegan EM,Lepenies B,Ruzal S,Kielian M,Martinez MG

    更新日期:2019-04-16 00:00:00

  • Food-bacteria interplay: pathometabolism of emetic Bacillus cereus.

    abstract::Bacillus cereus is a Gram-positive endospore forming bacterium known for its wide spectrum of phenotypic traits, enabling it to occupy diverse ecological niches. Although the population structure of B. cereus is highly dynamic and rather panmictic, production of the emetic B. cereus toxin cereulide is restricted to st...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.00704

    authors: Ehling-Schulz M,Frenzel E,Gohar M

    更新日期:2015-07-14 00:00:00

  • YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius.

    abstract::In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoa...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02084

    authors: Lemmens L,Tilleman L,De Koning E,Valegård K,Lindås AC,Van Nieuwerburgh F,Maes D,Peeters E

    更新日期:2019-09-10 00:00:00

  • A New Pathway for Mannitol Metabolism in Yeasts Suggests a Link to the Evolution of Alcoholic Fermentation.

    abstract::The yeasts belonging to the Wickerhamiella and Starmerella genera (W/S clade) share a distinctive evolutionary history marked by loss and subsequent reinstatement of alcoholic fermentation mediated by horizontal gene transfer events. Species in this clade also share unusual features of metabolism, namely the preferenc...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02510

    authors: Gonçalves C,Ferreira C,Gonçalves LG,Turner DL,Leandro MJ,Salema-Oom M,Santos H,Gonçalves P

    更新日期:2019-11-01 00:00:00

  • Factors influencing the diversity of iron uptake systems in aquatic microorganisms.

    abstract::Iron (Fe) is an essential micronutrient for many processes in all living cells. Dissolved Fe (dFe) concentrations in the ocean are of the order of a few nM, and Fe is often a factor limiting primary production. Bioavailability of Fe in aquatic environments is believed to be primarily controlled through chelation by Fe...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2012.00362

    authors: Desai DK,Desai FD,Laroche J

    更新日期:2012-10-18 00:00:00

  • A Review: The Styrene Metabolizing Cascade of Side-Chain Oxygenation as Biotechnological Basis to Gain Various Valuable Compounds.

    abstract::Styrene is one of the most produced and processed chemicals worldwide and is released into the environment during widespread processing. But, it is also produced from plants and microorganisms. The natural occurrence of styrene led to several microbiological strategies to form and also to degrade styrene. One pathway ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2018.00490

    authors: Oelschlägel M,Zimmerling J,Tischler D

    更新日期:2018-03-22 00:00:00

  • LAM Genes Contribute to Environmental Stress Tolerance but Sensibilize Yeast Cells to Azoles.

    abstract::Lam proteins transport sterols between the membranes of different cellular compartments. In Saccharomyces cerevisiae, the LAM gene family consists of three pairs of paralogs. Because the function of paralogous genes can be redundant, the phenotypes of only a small number of LAM gene deletions have been reported; thus,...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00038

    authors: Sokolov SS,Vorobeva MA,Smirnova AI,Smirnova EA,Trushina NI,Galkina KV,Severin FF,Knorre DA

    更新日期:2020-01-28 00:00:00

  • Identification of Diverse Integron and Plasmid Structures Carrying a Novel Carbapenemase Among Pseudomonas Species.

    abstract::A novel carbapenem-hydrolyzing beta-lactamase, called IMP-63, was identified in three clonally distinct strains of Pseudomonas aeruginosa and two strains of Pseudomonas putida isolated within a 4 year timeframe in three French hospitals. The blaIMP-63 gene that encodes this carbapenemase turned out to be located in th...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00404

    authors: Liapis E,Bour M,Triponney P,Jové T,Zahar JR,Valot B,Jeannot K,Plésiat P

    更新日期:2019-03-04 00:00:00

  • Host Range and Symbiotic Effectiveness of N2O Reducing Bradyrhizobium Strains.

    abstract::Emissions of the potent greenhouse gas N2O is one of the environmental problems associated with intensive use of synthetic N fertilizers, and novel N2O mitigation strategies are needed to minimize fertilizer applications and N2O release without affecting agricultural efficiencies. Increased incorporation of legume cro...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02746

    authors: Woliy K,Degefu T,Frostegård Å

    更新日期:2019-11-29 00:00:00

  • Soil Bacteria Isolated From Tunisian Arid Areas Show Promising Antimicrobial Activities Against Gram-Negatives.

    abstract::Arid regions show relatively fewer species in comparison to better-watered biomes, but the competition for the few nutrients is very distinct. Here, in total 373 bacterial strains were isolated from rhizospheric soils obtained from three different sampling sites in Tunisia. Their potential for the production of antimi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02742

    authors: Nasfi Z,Busch H,Kehraus S,Linares-Otoya L,König GM,Schäberle TF,Bachoual R

    更新日期:2018-11-13 00:00:00

  • Modeling of the ComRS Signaling Pathway Reveals the Limiting Factors Controlling Competence in Streptococcus thermophilus.

    abstract::In streptococci, entry in competence is dictated by ComX abundance. In Streptococcus thermophilus, production of ComX is transient and tightly regulated during growth: it is positively regulated by the cell-cell communication system ComRS during the activation phase and negatively regulated during the shut-off phase b...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01413

    authors: Haustenne L,Bastin G,Hols P,Fontaine L

    更新日期:2015-12-22 00:00:00

  • Who possesses drug resistance genes in the aquatic environment?: sulfamethoxazole (SMX) resistance genes among the bacterial community in water environment of Metro-Manila, Philippines.

    abstract::Recent evidence has shown that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Her...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2013.00102

    authors: Suzuki S,Ogo M,Miller TW,Shimizu A,Takada H,Siringan MA

    更新日期:2013-04-30 00:00:00

  • Embelin Restores Carbapenem Efficacy against NDM-1-Positive Pathogens.

    abstract::The emergence and spread of carbapenemase in Gram-negative pathogens poses an enormous threat to global public health. New Delhi metallo-β-lactamase-1 (NDM-1) inactivates nearly every class of β-lactam antibiotics, including carbapenem; however, there is no clinically useful NDM-1 inhibitor. Embelin, an important ingr...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00071

    authors: Ning NZ,Liu X,Chen F,Zhou P,Hu L,Huang J,Li Z,Huang J,Li T,Wang H

    更新日期:2018-01-25 00:00:00

  • Identification of New Degrons in Streptococcus mutans Reveals a Novel Strategy for Engineering Targeted, Controllable Proteolysis.

    abstract::Recently, controllable, targeted proteolysis has emerged as one of the most promising new strategies to study essential genes and otherwise toxic mutations. One of the principal limitations preventing the wider adoption of this approach is due to the lack of easily identifiable species-specific degrons that can be use...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02572

    authors: Liu N,Chaudhry MT,Xie Z,Kreth J,Merritt J

    更新日期:2017-12-19 00:00:00

  • Fermentation of Apple Juice with a Selected Yeast Strain Isolated from the Fermented Foods of Himalayan Regions and Its Organoleptic Properties.

    abstract::Twenty-three Saccharomyces cerevisiae strains isolated from different fermented foods of Western Himalayas have been studied for strain level and functional diversity in our department. Among these 23 strains, 10 S. cerevisiae strains on the basis of variation in their brewing traits were selected to study their organ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01012

    authors: Kanwar SS,Keshani

    更新日期:2016-06-28 00:00:00

  • The case for a rational genome-based vaccine against malaria.

    abstract::Historically, vaccines have been designed to mimic the immunity induced by natural exposure to the target pathogen, but this approach has not been effective for any parasitic pathogen of humans or complex pathogens that cause chronic disease in humans, such as Plasmodium. Despite intense efforts by many laboratories a...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2014.00741

    authors: Proietti C,Doolan DL

    更新日期:2015-01-22 00:00:00

  • 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.

    abstract::Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potentia...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00036

    authors: Baksi KD,Kuntal BK,Mande SS

    更新日期:2018-01-24 00:00:00

  • Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha).

    abstract::Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.592735

    authors: Freitas-Silva J,de Oliveira BFR,Vigoder FM,Muricy G,Dobson ADW,Laport MS

    更新日期:2021-01-08 00:00:00

  • Glass-forming property of hydroxyectoine is the cause of its superior function as a desiccation protectant.

    abstract::We were able to demonstrate that hydroxyectoine, in contrast to ectoine, is a good glass-forming compound. Fourier transform infrared and spin label electron spin resonance studies of dry ectoine and hydroxyectoine have shown that the superior glass-forming properties of hydroxyectoine result from stronger intermolecu...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2014.00150

    authors: Tanne C,Golovina EA,Hoekstra FA,Meffert A,Galinski EA

    更新日期:2014-04-04 00:00:00

  • Chemically-Mediated Interactions Between Macroalgae, Their Fungal Endophytes, and Protistan Pathogens.

    abstract::Filamentous fungi asymptomatically colonize the inner tissues of macroalgae, yet their ecological roles remain largely underexplored. Here, we tested if metabolites produced by fungal endophytes might protect their host against a phylogenetically broad spectrum of protistan pathogens. Accordingly, the cultivable funga...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.03161

    authors: Vallet M,Strittmatter M,Murúa P,Lacoste S,Dupont J,Hubas C,Genta-Jouve G,Gachon CMM,Kim GH,Prado S

    更新日期:2018-12-21 00:00:00

  • Sample Processing Methods Impacts on Rumen Microbiome.

    abstract::The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material t...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00861

    authors: Martinez-Fernandez G,Denman SE,McSweeney CS

    更新日期:2019-04-30 00:00:00

  • Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP).

    abstract::Dimethylsulfoniopropionate (DMSP) is a metabolite produced primarily by marine phytoplankton and is the main precursor to the climatically important gas dimethylsulfide (DMS). DMS is released upon bacterial catabolism of DMSP, but it is not the only possible fate of DMSP sulfur. An alternative demethylation/demethiola...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2011.00172

    authors: Reisch CR,Moran MA,Whitman WB

    更新日期:2011-08-12 00:00:00

  • Differential Regulation of Myeloid-Derived Suppressor Cells by Candida Species.

    abstract::Myeloid-derived suppressor cells (MDSCs) are innate immune cells characterized by their ability to suppress T-cell responses. Recently, we demonstrated that the human-pathogenic fungi Candida albicans and Aspergillus fumigatus induced a distinct subset of neutrophilic MDSCs. To dissect Candida-mediated MDSC induction ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01624

    authors: Singh A,Lelis F,Braig S,Schäfer I,Hartl D,Rieber N

    更新日期:2016-10-13 00:00:00

  • Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests.

    abstract::In Appalachian ecosystems, forest disturbance has long-term effects on microbially driven biogeochemical processes such as nitrogen (N) cycling. However, little is known regarding long-term responses of forest soil microbial communities to disturbance in the region. We used 16S and ITS sequencing to characterize soil ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02872

    authors: Osburn ED,McBride SG,Aylward FO,Badgley BD,Strahm BD,Knoepp JD,Barrett JE

    更新日期:2019-12-11 00:00:00

  • Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria.

    abstract::We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphe...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00980

    authors: Els N,Greilinger M,Reisecker M,Tignat-Perrier R,Baumann-Stanzer K,Kasper-Giebl A,Sattler B,Larose C

    更新日期:2020-05-20 00:00:00

  • Family Aggregation of HTLV-1 Infection Associated with FAS -670A/G Polymorphism: A Case Report.

    abstract::Human T-lymphotropic virus 1 (HTLV-1) infection has been associated with ATL and inflammatory diseases but remains a neglected health problem. HTLV-1 associated diseases were originally described as sporadic entities, but family aggregations have been reported. Viral, genetic, immunological and behavioral factors were...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02685

    authors: Vallinoto ACR,Santana BB,Queiroz MAF,da Silva ANMR,Cayres-Vallinoto IMV,da Costa CA,de Sousa MS,Ishak R

    更新日期:2018-01-15 00:00:00

  • Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem-Resistant Acinetobacter baumannii.

    abstract::Two lytic bacteriophages, WCHABP1 and WCHABP12, were recovered from hospital sewage and were able to infect 9 and 12 out of 18 carbapenem-resistant Acinetobacter baumannii clinical strains, which belonged to different clones. Electron microscopy scan showed that both bacteriophages had the similar morphology as those ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00850

    authors: Zhou W,Feng Y,Zong Z

    更新日期:2018-04-30 00:00:00

  • Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains.

    abstract::Swine grown under commercial conditions are vulnerable to environmental exposure to several viruses, which may cause infectious diseases and spread easily and rapidly, resulting in significant economic losses in animal husbandry. Previous studies have suggested that probiotics seem to be a new and promising alternativ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01578

    authors: Chang-Liao WP,Lee A,Chiu YH,Chang HW,Liu JR

    更新日期:2020-07-15 00:00:00

  • Antimicrobial Metabolites Produced by Penicillium mallochii CCH01 Isolated From the Gut of Ectropis oblique, Cultivated in the Presence of a Histone Deacetylase Inhibitor.

    abstract::Three chemical epigenetic modifiers [5-azacytidine, nicotinamide, and suberoylanilide hydroxamic acid (SAHA)] were applied to induce the metabolites of Penicillium mallochii CCH01, a fungus isolated from the gut of Ectropis oblique. Metabolite profiles of P. mallochii CCH01 were obviously changed by SAHA treatment. Fo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02186

    authors: Zhang S,Fang H,Yin C,Wei C,Hu J,Zhang Y

    更新日期:2019-10-02 00:00:00