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OBJECTIVES: The adenoid pad, which is located between the orifice of the Eustachian tube (ET) and posterior nasal cavity, can affect the development of otitis media with effusion (OME) because of its anatomical location. The aim of the present study was to evaluate adenoid microbial colonization through 16S ribosomal RNA (rRNA) pyrosequencing, an advanced molecular technique, and to document the relationship with OME. MATERIALS and METHODS: Adenoid samples were collected using sterile cotton from 32 children during ventilation tube insertion. Sixteen children with OME who underwent tonsillectomy and adenoidectomy due to obstructive symptoms were assigned to the OME group and sixteen children without OME were assigned to the control group. We performed a 16S rRNA-based culture-independent survey of bacterial communities using the MiSeq platform. RESULTS: The diversity index, mean operational taxonomic units, and Shannon index were lower in the OME group than those in the control group. A taxonomic analysis showed differences in microbiota distribution between the OME and control groups at the phylum, genus, and species levels. The analysis, which was based on weighted UniFrac distances, revealed differences in microbial composition between the two groups. CONCLUSION: Bacterial community analysis using 16S rRNA pyrosequencing allows us to understand the relationship between the microbial communities of adenoids and the development of OME better. KEYWORDS: Otitis media, microbiome, adenoid

Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile . Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile . We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation. The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile ( C. difficile ) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.

Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers' skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates' skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.

The microbiota has been shown to promote intestinal tumourigenesis, but a possible anti-tumourigenic effect has also been postulated. Here, we demonstrate that changes in the microbiota and mucus composition are concomitant with tumourigenesis. We identified two anti-tumourigenic strains of the microbiota— Faecalibaculum rodentium and its human homologue, Holdemanella biformis —that are strongly under-represented during tumourigenesis. Reconstitution of Apc Min/+ or azoxymethane- and dextran sulfate sodium-treated mice with an isolate of F. rodentium ( F . PB1) or its metabolic products reduced tumour growth. Both F . PB1 and H. biformis produced short-chain fatty acids that contributed to control protein acetylation and tumour cell proliferation by inhibiting calcineurin and NFATc3 activation in mouse and human settings. We have thus identified endogenous anti-tumourigenic bacterial strains with strong diagnostic, therapeutic and translational potential. The murine gut commensal Faecalibaculum rodentium and its human homologue, Holdemanella biformis , are under-represented in tumour development and can reduce tumour progression via short-chain fatty acid production, providing insights into a protective microbial candidate.

The effects of neonatal immunization with 7-valent pneumococcal conjugate vaccine (7vPCV) on development of T-cell memory and general immune maturation were studied in a cohort of Papua New Guinean newborns. Neonatal 7vPCV priming (followed by a dose at 1 and 2 months of age) was associated with enhanced Th2, but not Th1, cytokine responses to CRM197 compared to 7vPCV at 1 and 2 months of age only. T cell responses to non-7vPCV vaccine antigens were similar in all groups, but TLR-mediated IL-6 and IL-10 responses were enhanced in 7vPCV vaccinated compared to controls. Neonatal 7vPCV vaccination primes T cell responses with a polarization towards Th2 with no bystander effects on other T cell responses.

Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction.

Determining bacterial gene expression during infection is fundamental to understand pathogenesis. In this study, we used dual RNA-seq to simultaneously measure P. aeruginosa and the murine host’s gene expression and response to respiratory infection. Bacterial genes encoding products involved in metabolism and virulence were differentially expressed during infection and the type III and VI secretion systems were highly expressed in vivo . Strikingly, heme acquisition, ferric-enterobactin transport, and pyoverdine biosynthesis genes were found to be significantly up-regulated during infection. In the mouse, we profiled the acute immune response to P. aeruginosa and identified the pro-inflammatory cytokines involved in acute response to the bacterium in the lung. Additionally, we also identified numerous host iron sequestration systems upregulated during infection. Overall, this work sheds light on how P. aeruginosa triggers a pro-inflammatory response and competes for iron with the host during infection, as iron is one of the central elements for which both pathogen and host fight during acute pneumonia.

Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice Patrice D. Cani 1 2 , Rodrigo Bibiloni 3 , Claude Knauf 2 , Aurélie Waget 2 , Audrey M. Neyrinck 1 , Nathalie M. Delzenne 1 and Rémy Burcelin 2 1 Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Université catholique de Louvain, Brussels, Belgium 2 Rangueil Institute of Molecular Medicine, Toulouse, France 3 Nestlé Research Center, Department of Nutrition and Health, Lausanne, Switzerland Corresponding author: Prof. Rémy Burcelin, Rangueil Institute of Molecular Medicine, I 2 MR, IFR31, Toulouse, France. E-mail: burcelin{at}toulouse.inserm.fr Abstract OBJECTIVE— Diabetes and obesity are characterized by a low-grade inflammation whose molecular origin is unknown. We previously determined, first, that metabolic endotoxemia controls the inflammatory tone, body weight gain, and diabetes, and second, that high-fat feeding modulates gut microbiota and the plasma concentration of lipopolysaccharide (LPS), i.e., metabolic endotoxemia. Therefore, it remained to demonstrate whether changes in gut microbiota control the occurrence of metabolic diseases. RESEARCH DESIGN AND METHODS— We changed gut microbiota by means of antibiotic treatment to demonstrate, first, that changes in gut microbiota could be responsible for the control of metabolic endotoxemia, the low-grade inflammation, obesity, and type 2 diabetes and, second, to provide some mechanisms responsible for such effect. RESULTS— We found that changes of gut microbiota induced by an antibiotic treatment reduced metabolic endotoxemia and the cecal content of LPS in both high-fat–fed and ob/ob mice. This effect was correlated with reduced glucose intolerance, body weight gain, fat mass development, lower inflammation, oxidative stress, and macrophage infiltration marker mRNA expression in visceral adipose tissue. Importantly, high-fat feeding strongly increased intestinal permeability and reduced the expression of genes coding for proteins of the tight junctions. Furthermore, the absence of CD14 in ob/ob CD14 − / − mutant mice mimicked the metabolic and inflammatory effects of antibiotics. CONCLUSIONS— This new finding demonstrates that changes in gut microbiota controls metabolic endotoxemia, inflammation, and associated disorders by a mechanism that could increase intestinal permeability. It would thus be useful to develop strategies for changing gut microbiota to control, intestinal permeability, metabolic endotoxemia, and associated disorders. DGGE, denaturing gradient gel electrophoresis FITC, fluorescein isothiocyanate IL, interleukin LPS, lipopolysaccharide MDA, malondialdehyde MCP, monocyte chemotactic protein PAI-1, plasminogen activator inhibitor 1 RPL19, ribosomal protein L19 TBARS, thiobarbituric acid reactive substances TNF-α, tumor necrosis factor-α ZO-1, zonula occludens-1 Footnotes Published ahead of print at http://diabetes.diabetesjournals.org on 27 February 2008. DOI: 10.2337/db07-1403. Additional information for this article can be found in an online appendix at http://dx.doi.org/10.2337/db07-1403 . The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. Accepted February 25, 2008. Received October 3, 2007. DIABETES

Multidrug resistant organisms are a serious threat to human health 1 , 2 . Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying multidrug resistant organisms increase mortality 3 , 4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution 5 , require several days before informing key clinical decisions. Rapid AST would transform the care of patients with infection while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here we describe a rapid assay for combined genotypic and phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 h faster than standard workflows, with <4 h assay time on a pilot instrument for hybridization-based multiplexed RNA detection implemented directly from positive blood cultures. A new assay combining genotypic and phenotypic information accelerates accurate clinical antibiotic susceptibility testing.

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.