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Host-Microbe Biology

  • Open Access
    Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome
    Methods and Protocols | Host-Microbe Biology
    Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

    Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific...

    Florencia A. Tettamanti Boshier, Sujatha Srinivasan, Anthony Lopez, Noah G. Hoffman, Sean Proll, David N. Fredricks, Joshua T. Schiffer
  • Open Access
    Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth
    Research Article | Host-Microbe Biology
    Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth

    Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the...

    Léo Gerlin, Ludovic Cottret, Sophie Cesbron, Géraldine Taghouti, Marie-Agnès Jacques, Stéphane Genin, Caroline Baroukh
  • Open Access
    The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics
    Research Article | Host-Microbe Biology
    The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics

    Gut microbiota is considered to play a role in disease progression, and previous studies have reported an association of microbiome dysbiosis with T2D. In this study, we have attempted to investigate gut microbiota of ND, PreDMs, NewDMs, and KnownDMs. We found that the genera Akkermansia and Blautia decreased significantly (P < 0.05) in treatment-naive diabetics and were restored in KnownDMs on antidiabetic...

    Akshay H. Gaike, Dhiraj Paul, Shrikant Bhute, Dhiraj P. Dhotre, Pranav Pande, Smitha Upadhyaya, Yugandhar Reddy, Ramya Sampath, Debjani Ghosh, D. Chandraprabha, Jhankar Acharya, Gautam Banerjee, Vilas P. Sinkar, Saroj S. Ghaskadbi, Yogesh S. Shouche
  • Open Access
    Depletion of <em>Blautia</em> Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening
    Research Article | Host-Microbe Biology
    Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening

    Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin...

    Alfonso Benítez-Páez, Eva M. Gómez del Pugar, Inmaculada López-Almela, Ángela Moya-Pérez, Pilar Codoñer-Franch, Yolanda Sanz
  • Open Access
    Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation
    Editor's Pick Research Article | Host-Microbe Biology
    Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation

    The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive...

    Simone Rampelli, Matteo Soverini, Federica D’Amico, Monica Barone, Teresa Tavella, Daniela Monti, Miriam Capri, Annalisa Astolfi, Patrizia Brigidi, Elena Biagi, Claudio Franceschi, Silvia Turroni, Marco Candela
  • Open Access
    Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
    Research Article | Host-Microbe Biology
    Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

    Public interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented...

    Bryn C. Taylor, Franck Lejzerowicz, Marion Poirel, Justin P. Shaffer, Lingjing Jiang, Alexander Aksenov, Nicole Litwin, Gregory Humphrey, Cameron Martino, Sandrine Miller-Montgomery, Pieter C. Dorrestein, Patrick Veiga, Se Jin Song, Daniel McDonald, Muriel Derrien, Rob Knight
  • Open Access
    The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation
    Research Article | Host-Microbe Biology
    The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation

    The gut microbiome may play an important role in insect-plant interactions mediated by plant secondary metabolites, but the microbial communities and functions of toxic plant feeders are still poorly characterized. In the present study, we provide the first metagenome of gut bacterial communities associated with a specialist weevil feeding on saponin-rich and saponin-low camellia seeds, and the results reveal the correlation between...

    Shouke Zhang, Jinping Shu, Huaijun Xue, Wei Zhang, Yabo Zhang, Yaning Liu, Linxin Fang, Yangdong Wang, Haojie Wang
  • Open Access
    Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?
    Letter to the Editor | Host-Microbe Biology
    Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?
    Christopher Kenyon
  • Open Access
    Reply to Kenyon, “Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?”
    Author Reply | Host-Microbe Biology
    Reply to Kenyon, “Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?”
    Yaohua Yang, Wei Zheng, Qiuyin Cai, Martha J. Shrubsole, Zhiheng Pei, Robert Brucker, Mark Steinwandel, Seth R. Bordenstein, Zhigang Li, William J. Blot, Xiao-Ou Shu, Jirong Long
  • Open Access
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
    Research Article | Host-Microbe Biology
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

    Metabolome-informed analyses can enhance omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate here the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an...

    Julia M. Gauglitz, James T. Morton, Anupriya Tripathi, Shalisa Hansen, Michele Gaffney, Carolina Carpenter, Kelly C. Weldon, Riya Shah, Amy Parampil, Andrea L. Fidgett, Austin D. Swafford, Rob Knight, Pieter C. Dorrestein

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