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Host-Microbe Biology

  • Open Access
    Formula Diet Alters the Ileal Metagenome and Transcriptome at Weaning and during the Postweaning Period in a Porcine Model
    Research Article | Host-Microbe Biology
    Formula Diet Alters the Ileal Metagenome and Transcriptome at Weaning and during the Postweaning Period in a Porcine Model

    Exclusive human milk (HM) breastfeeding for the first 6 months of age in infants is recommended to improve health outcomes during early life and beyond. When women are unable to provide sufficient HM, milk formula (MF) is often recommended as a complementary or alternative source of nutrition. Previous studies in piglets demonstrated that MF alters the gut microbiome and induces inflammatory cytokine production. The links between MF...

    Ahmed A. Elolimy, Charity Washam, Stephanie Byrum, Celine Chen, Harry Dawson, Anne K. Bowlin, Christopher E. Randolph, Manish K. Saraf, Laxmi Yeruva
  • Open Access
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
    Research Article | Host-Microbe Biology
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

    It is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization of multiple open source software tools. We present Bactopia, a pipeline for bacterial genome analysis, as an option for processing bacterial genome data. Bactopia also automates downloading of data from multiple public sources and species-specific customization. Because the pipeline...

    Robert A. Petit, Timothy D. Read
  • Open Access
    A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
    Research Article | Host-Microbe Biology
    A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

    To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome...

    Maria I. Rojas, Giselle S. Cavalcanti, Katelyn McNair, Sean Benler, Amanda T. Alker, Ana G. Cobián-Güemes, Melissa Giluso, Kyle Levi, Forest Rohwer, Barbara A. Bailey, Sinem Beyhan, Robert A. Edwards, Nicholas J. Shikuma
  • Open Access
    Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
    Research Article | Host-Microbe Biology
    Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin

    Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our “Western”-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in...

    Damien J. Cabral, Jenna I. Wurster, Benjamin J. Korry, Swathi Penumutchu, Peter Belenky
  • Open Access
    Host Genetic Factors Associated with Vaginal Microbiome Composition in Kenyan Women
    Research Article | Host-Microbe Biology
    Host Genetic Factors Associated with Vaginal Microbiome Composition in Kenyan Women

    Globally, bacterial vaginosis (BV) is a common condition in women. BV is associated with poorer reproductive health outcomes and HIV risk. Typically, BV represents a shift in the vaginal microbiome from one that is dominated by Lactobacillus to one that is diverse. Despite many women having similar exposures, the prevalence of BV and nonoptimal vaginal microbiome is increased for women of African descent, suggesting a possible...

    Supriya D. Mehta, Drew R. Nannini, Fredrick Otieno, Stefan J. Green, Walter Agingu, Alan Landay, Yinan Zheng, Lifang Hou
  • Open Access
    COVID-19 and the Gut Microbiome: More than a Gut Feeling
    Perspective | Host-Microbe Biology
    COVID-19 and the Gut Microbiome: More than a Gut Feeling

    Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include characterizations of the gut microbiome in clinical trials and studies that aim to broaden our understanding of coronavirus disease 2019 (COVID-19). Understanding the “gut-lung axes,” where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut...

    Daniel van der Lelie, Safiyh Taghavi
  • Open Access
    Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during <em>In Vitro</em> Fertilization Surgery
    Research Article | Host-Microbe Biology
    Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during In Vitro Fertilization Surgery

    The microbiome had been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction before the first success in IVF, while the data supporting or refuting this hypothesis were less than conclusive. Thanks to sequencing data from the 16S rRNA subunit, we characterized the microbiome in the reproductive tract of infertile women, and we found that changes in the vaginal microbiome are related to female...

    Changying Zhao, Zefeng Wei, Junjie Yang, Jiaming Zhang, Chunna Yu, Aijun Yang, Min Zhang, Lin Zhang, Ye Wang, Xiaofeng Mu, Xueyuan Heng, Huijun Yang, Zhongtao Gai, Xuenan Wang, Lei Zhang
  • Open Access
    Host and Parasite Transcriptomic Changes upon Successive <span class="named-content genus-species" id="named-content-1">Plasmodium falciparum</span> Infections in Early Childhood
    Research Article | Host-Microbe Biology
    Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood

    We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts.

    Katie R. Bradwell, Drissa Coulibaly, Abdoulaye K. Koné, Matthew B. Laurens, Ahmadou Dembélé, Youssouf Tolo, Karim Traoré, Amadou Niangaly, Andrea A. Berry, Bourema Kouriba, Christopher V. Plowe, Ogobara K. Doumbo, Kirsten E. Lyke, Shannon Takala-Harrison, Mahamadou A. Thera, Mark A. Travassos, David Serre
  • Open Access
    Genomic Analysis of Bovine <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
    Research Article | Host-Microbe Biology
    Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis

    Staphylococcus aureus is a major cause of bovine intramammary infections, leading to significant economic losses to dairy industry in Canada and worldwide. There is a lack of knowledge regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus...

    Sohail Naushad, Diego B. Nobrega, S. Ali Naqvi, Herman W. Barkema, Jeroen De Buck
  • Open Access
    Impact of the Novel Prophage ϕSA169 on Persistent Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Endovascular Infection
    Research Article | Host-Microbe Biology
    Impact of the Novel Prophage ϕSA169 on Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection

    Bacteriophages are viruses that invade the bacterial host, disrupt bacterial metabolism, and cause the bacterium to lyse. Because of its remarkable antibacterial activity and unique advantages over antibiotics, for instance, bacteriophage is specific for one species of bacteria and resistance to phage is less common than resistance to antibiotics. Indeed, bacteriophage therapy for treating infections due to multidrug-resistant pathogens...

    Liang Li, Genzhu Wang, Yi Li, Patrice Francois, Arnold S. Bayer, Liang Chen, Kati Seidl, Ambrose Cheung, Yan Q. Xiong

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