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microbiome

  • Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiomes of <em>Sorghum bicolor</em>
    Plant Microbiology
    Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiomes of Sorghum bicolor

    While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, very little has been published on how the corresponding crop plant microbiome is impacted.

    Heidi M.-L. Wipf, Ling Xu, Cheng Gao, Hannah B. Spinner, John Taylor, Peggy Lemaux, Jeffrey Mitchell, Devin Coleman-Derr
  • A Viability Quantitative PCR Dilemma: Are Longer Amplicons Better?
    Genetics and Molecular Biology
    A Viability Quantitative PCR Dilemma: Are Longer Amplicons Better?

    Viability quantitative PCR (v-qPCR) has evolved into a valuable, mainstream technique for determining the number of viable microorganisms in samples by qPCR. Amplicon length is known to be positively correlated with the ability to distinguish between live and dead bacteria but is negatively correlated with qPCR efficiency.

    Wannes Van Holm, Justien Ghesquière, Nico Boon, Tim Verspecht, Kristel Bernaerts, Naiera Zayed, Ioanna Chatzigiannidou, Wim Teughels
  • Mucin as a Functional Niche Is a More Important Driver of <em>In Vitro</em> Gut Microbiota Composition and Functionality than <span class="named-content genus-species" id="named-content-1">Akkermansia muciniphila</span> Supplementation
    Microbial Ecology
    Mucin as a Functional Niche Is a More Important Driver of In Vitro Gut Microbiota Composition and Functionality than Akkermansia muciniphila Supplementation

    Research into the identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health has put Akkermansia muciniphila in the spotlight. As a mucin degrader, A. muciniphila colonizes the interesting but not fully described host-glycan degradation niche. Much of research concerning A. muciniphila...

    Florence Van Herreweghen, Kim De Paepe, Massimo Marzorati, Tom Van de Wiele
  • Open Access
    Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to <em>Salmonella</em> Contamination of Alfalfa Seeds
    Food Microbiology
    Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds

    Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives.

    Jie Zheng, Elizabeth Reed, Padmini Ramachandran, Andrea Ottesen, Eric W. Brown, Yu Wang
  • Microbiome Variability across the Native and Invasive Ranges of the Ascidian <span class="named-content genus-species" id="named-content-1">Clavelina oblonga</span>
    Invertebrate Microbiology
    Microbiome Variability across the Native and Invasive Ranges of the Ascidian Clavelina oblonga

    Nonnative species destabilize coastal ecosystems and microbial symbionts may facilitate their spread by enhancing host survival and fitness. However, we know little of the microorganisms that live inside invasive species and whether they change as the host spreads to new areas. In this study, we investigated the microbial communities of an introduced ascidian (Clavelina oblonga) and tracked symbiont changes across locations...

    Millie Goddard-Dwyer, Susanna López-Legentil, Patrick M. Erwin
  • Open Access
    Gut Bacteria Mediate Nutrient Availability in <em>Drosophila</em> Diets
    Invertebrate Microbiology
    Gut Bacteria Mediate Nutrient Availability in Drosophila Diets

    Both in the laboratory and in nature, D. melanogaster-associated microbes serve as nutritional effectors, either through the production of metabolites or as direct sources of protein biomass. The relationship between the microbiome and the resulting host nutritional physiology is significantly impacted by diet composition, yet studies involving...

    Danielle N. A. Lesperance, Nichole A. Broderick
  • Open Access
    Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses
    Minireview
    Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses

    Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and...

    Tasha M. Santiago-Rodriguez, Emily B. Hollister
  • Impact of the Human Microbiome in Forensic Sciences: a Systematic Review
    Minireview | Spotlight
    Impact of the Human Microbiome in Forensic Sciences: a Systematic Review

    Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible...

    Manuel G. García, María D. Pérez-Cárceles, Eduardo Osuna, Isabel Legaz
  • Dietary Supplementation with Sodium Sulfate Improves Rumen Fermentation, Fiber Digestibility, and the Plasma Metabolome through Modulation of Rumen Bacterial Communities in Steers
    Biotechnology
    Dietary Supplementation with Sodium Sulfate Improves Rumen Fermentation, Fiber Digestibility, and the Plasma Metabolome through Modulation of Rumen Bacterial Communities in Steers

    Essential elements like nitrogen and sulfur greatly affect rumen fermentation and metabolism in ruminants. However, little knowledge is available on the effects of sulfur on the rumen microbiota and plasma metabolome. The results of the present trial demonstrated that supplementing the steer ration with sodium sulfate markedly improved rumen fermentation, fiber digestibility, and metabolism of amino acids, purine derivatives, and...

    Yuchao Zhao, Biao Xie, Jian Gao, Guangyong Zhao
  • Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat
    Microbial Ecology
    Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat

    Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a light on this topic as we investigate how the phylogenetic structure of microbial communities...

    François-Étienne Sylvain, Aleicia Holland, Sidki Bouslama, Émie Audet-Gilbert, Camille Lavoie, Adalberto Luis Val, Nicolas Derome

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