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Olfactory dysfunction is a pre-motor symptom of Parkinson’s disease (PD) that appears years prior to diagnosis and can affect quality of life in PD. Changes in microbiota community in deep nasal cavity near the olfactory bulb may trigger the olfactory bulb-mediated neuroinflammatory cascade and eventual dopamine loss in PD. To determine if the deep nasal cavity microbiota of PD is significantly altered in comparison to healthy controls, we characterized the microbiota of the deep nasal cavity using 16S rRNA gene amplicon sequencing in PD subjects and compared it to that of spousal and non-spousal healthy controls. Correlations between microbial taxa and PD symptom severity were also explored. Olfactory microbial communities of PD individuals were more similar to those of their spousal controls than to non-household controls. In direct comparison of PD and spousal controls and of PD and non-spousal controls, significantly differently abundant taxa were identified, and this included increased relative abundance of putative opportunistic-pathobiont species such as Moraxella catarrhalis. M. catarrhalis was also significantly correlated with more severe motor scores in PD subjects. This proof-of-concept study provides evidence that potential pathobionts are detected in the olfactory bulb and that a subset of changes in the PD microbiota community could be a consequence of unique environmental factors associated with PD living. We hypothesize that an altered deep nasal microbiota, characterized by a putative pro-inflammatory microbial community, could trigger neuroinflammation in PD.

Background A critical role for host-microbe interactions and establishment of vaccine responses has been postulated. Human milk oligosaccharides, of which 2′-fucosyllactose (2′FL) is the most prevalent, are known to alter host-associated microbial communities and play a critical role in the immunologic development of breastfed infants. Objectives Dietary supplementation with a combination of 2′FL and prebiotic short-chain (sc) galacto-oligosaccharides (GOS) and long-chain (lc) fructo-oligosaccharides (FOS) was employed to examine human milk oligosaccharide effects on immune responsiveness, within a murine influenza vaccination model. Methods Female mice (6 wk old, C57Bl/6JOlaHsd) were fed either control diet (CON) or scGOS/lcFOS/2′FL-containing diet (GF2F) for 45 d. After starting dietary intervention (day 14), mice received a primary influenza vaccination (day 0) followed by a booster vaccination (day 21), after which ear challenges were conducted to measure vaccine-specific delayed type hypersensitivity (DTH). Serum immunoglobulin (Ig) levels, fecal and cecal microbial community structure, short-chain fatty acids, host intestinal gene expression and cellular responses in the mesenteric lymph nodes (MLNs) were also measured. Results Relative to CON, mice fed the GF2F diet had increased influenza vaccine–specific DTH responses (79.3%; P

Additional file 2 Fig. S2. Profile of three most abundant liver bile acids from control and berberine treated mice.

Additional file 5 Fig. S5. 16S rDNA profile of human gut bacterial consortium in cecal samples of gnotobiotic fed control diet versus berberine. A. Relative abundance of bacterial families in control mice (C1-C6) and berberine treatment (B1-B6) B. Non-metric multidimensional scaling (NMDS) plot of beta diversity based on Bray-Curtis index. ANOSIM test results: R = 0.141, P = 0.123, 999 permutations.

Additional file 1 Fig. S1. Profile of liver bile acids from control and berberine treated mice.

Additional file 4 Fig. S4. Profile of cecal bile acids between control and berberine treated mice not represented in Fig. 1. Significance determined by student t test. * P

Additional file 3 Fig. S3. Serum bile acid profile in control and berberine treated mice.

Additional file 1: Supplementary Table 1. Demographics and clinical characteristics of COVID-19-positive individuals. Supplementary Table 2. Alpha-diversity values in nasopharyngeal samples. Supplementary Table 3. Global community analysis of nasopharyngeal microbial community structure in COVID-19-positive and -negative patients, as assessed by Permutational Multivariate Analyses of Variance (PERMANOVA). Supplementary Table4. Relative abundances of bacterial taxa in COVID-19-positive and -negative nasopharyngeal samples. Supplementary Table 5. Differential relative abundance of nasopharyngeal bacterial phyla in COVID-19-positive and -negative samples identified by DESeq2 analysis. Supplementary Table 6. Genus taxonomic level differential abundance DeSeq2 analysis between COVID-19-positive and -negative patient’s nasopharyngeal samples.

Additional file 6 Fig. S6. Shannon Index comparison between control mice and berberine treatment. The rarified 23,900 MiSeq dataset was used. Mann-Whitney test P = 0.309.

The composition and activity of the intestinal microbial community structures can be beneficially modulated by nutritional components such as non-digestible oligosaccharides and omega-3 poly-unsaturated fatty acids (n-3 PUFAs). These components affect immune function, brain development and behaviour. We investigated the additive effect of a dietary combination of scGOS:lcFOS and n-3 PUFAs on caecal content microbial community structures and development of the immune system, brain and behaviour from day of birth to early adulthood in healthy mice. Male BALB/cByJ mice received a control or enriched diet with a combination of scGOS:lcFOS (9:1) and 6% tuna oil (n-3 PUFAs) or individually scGOS:lcFOS (9:1) or 6% tuna oil (n-3 PUFAs). Behaviour, caecal content microbiota composition, short-chain fatty acid levels, brain monoamine levels, enterochromaffin cells and immune parameters in the mesenteric lymph nodes (MLN) and spleen were assessed. Caecal content microbial community structures displayed differences between the control and dietary groups, and between the dietary groups. Compared to control diet, the scGOS:lcFOS and combination diets increased caecal saccharolytic fermentation activity. The diets enhanced the number of enterochromaffin cells. The combination diet had no effects on the immune cells. Although the dietary effect on behaviour was limited, serotonin and serotonin metabolite levels in the amygdala were increased in the combination diet group. The combination and individual interventions affected caecal content microbial profiles, but had limited effects on behaviour and the immune system. No apparent additive effect was observed when scGOS:lcFOS and n-3 PUFAs were combined. The results suggest that scGOS:lcFOS and n-3 PUFAs together create a balance—the best of both in a healthy host.

Additional file 1: Figure S1. Non-metric multidimensional scaling (nMDS) based on the Bray-Curtis dissimilarity index of the SEED annotated gene counts for (a) metagenome, and (b) metatranscriptome. Figure S2. Correlation between metagenomics enriched SEED categories and soil environmental parameters, for (a) subsystems enriched in TWW irrigated roots, or (b) enriched in FW irrigated roots. Figure S3. Metagenomic enriched KEGG modules in (a) FW irrigated roots, or (b) TWW irrigated roots. The bar chart present the log10(P value) of the enrichment analysis calculated by KeggProfiler ‘R’ package. Figure S4. Metatransctiptome enrichement KEGG modules in (a) FW irrigated roots, or (b) TWW irrigated roots. The bar chart present the log10(P value) of the enrichment analysis calculated by KeggProfiler ‘R’ package. Figure S5. Microbial gene expression patterns revealed TWW irrigation enrichment of arginine and proline metabolism genes, highlighting those in the arginine-to-spermidine pathway (colored in pink). Figure S6. Meta- analysis of the full nqr operon in environmental metagenomes. Box plot demonstrates the nqr operon (a-f subunits) gene abundance in acidic pH (8) pH. Figure S7. Meta- analysis of the full mnh operon in environmental metagenomes. Box plot demonstrates the mnh operon (a-g subunits) gene abundance in acidic pH (8) pH.

Supplemental Material, sj-pdf-1-std-10.1177_0956462420985973 for Schistosomiasis is associated with rectal mucosal inflammation among Kenyan men who have sex with men by Supriya D Mehta, Duncan Okal, Fredrick Otieno, Stefan J Green, Rachel K Nordgren, Sanja Huibner, Robert C Bailey, Dulal K Bhaumik, Alan Landay and Rupert Kaul in International Journal of STD & AIDS

Supplemental Material, sj-pdf-1-std-10.1177_0956462420985973 for Schistosomiasis is associated with rectal mucosal inflammation among Kenyan men who have sex with men by Supriya D Mehta, Duncan Okal, Fredrick Otieno, Stefan J Green, Rachel K Nordgren, Sanja Huibner, Robert C Bailey, Dulal K Bhaumik, Alan Landay and Rupert Kaul in International Journal of STD & AIDS

© 2017 Wen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2 ±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (1-3%, p