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Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.

Background and purpose: The role of the gut microbiome in the pathogenesis of Parkinson disease (PD) is under intense investigation, and the results presented are still very heterogeneous. These discrepancies arise not only from the highly heterogeneous pathology of PD, but also from widely varying methodologies at all stages of the workflow, from sampling to final statistical analysis. The aim of the present work is to harmonize the workflow across studies to reduce the methodological heterogeneity and to perform a pooled analysis to account for other sources of heterogeneity. Methods: We performed a systematic review to identify studies comparing the gut microbiota of PD patients to healthy controls. A workflow was designed to harmonize processing across all studies from bioinformatics processing to final statistical analysis using a Bayesian random‐effects meta‐analysis based on individual patient‐level data. Results: The results show that harmonizing workflows minimizes differences between statistical methods and reveals only a small set of taxa being associated with the pathogenesis of PD. Increased shares of the genera Akkermansia and Bifidobacterium and decreased shares of the genera Roseburia and Faecalibacterium were most characteristic for PD‐associated microbiota. Conclusions: Our study summarizes evidence that reduced levels of butyrate‐producing taxa in combination with possible degradation of the mucus layer by Akkermansia may promote intestinal inflammation and reduced permeability of the gut mucosal layer. This may allow potentially pathogenic metabolites to transit and enter the enteric nervous system. [ABSTRACT FROM AUTHOR]

Growth of Vibrio cholerae O1 Ogawa Eltor was studied with a growth assay in which autoclaved and filtered (0.22 [micro]m) freshwater was inoculated at low cell density (5 x [10.sup.3] cells [ml.sup.-1]) and proliferation was followed with flow cytometry. Against the common view, V. cholerae was able to grow extensively in different kinds of freshwater. The bacterium multiplied in river water, lake water and effluent of a wastewater treatment plant up to a cell density of 1.55x [10.sup.6] cells [ml.sup.-1]. In these samples, apparent assimilable organic carbon ([AOC.sub.app]) concentrations ranged from 52 up to 800 [micro]g [l.sup.-1] and the results demonstrate a positive trend between the [AOC.sub.app] concentration and final cell concentration, suggesting that AOC was a key parameter governing growth of V. cholerae. No growth was observed in waters (tap and bottled drinking water) containing less than approximately 60 [micro]g [AOC.sub.app] [l.sup.-1]. When pure cultures of V. cholerae were grown on identical lake water at different temperatures (20, 25 and 30 [degrees]C) the maximum specific growth rates ([[micro].sub.max]) achieved were 0.22 [h.sup.-1], 0.32 [h.sup.-1] and 0.45 [h.sup.-1], respectively. In addition, growth was characterized in lake water samples amended with different concentrations of NaCl. The highest [[micro].sub.max] of V. cholerae was recorded at moderate salinity levels (5 g NaCl [l.sup.-1], [[micro].sub.max] = 0.84 [h.sup.-1]), whereas at 30 g NaCl [l.sup.-1] ([[micro].sub.max] = 0.30 [h.sup.-1]) or 0 g NaCl [l.sup.-1] ([[micro].sub.max] = 0.40 [h.sup.-1]) specific growth rates were significantly reduced. In the water tested here, [[micro].sub.max] of V. cholerae was always around 50% of that exhibited by a freshwater community of indigenous bacteria enriched from the water sampling site. Direct batch competition experiments between V. cholerae and the lake water bacterial community were performed at different temperatures in which V. cholerae was enumerated in the total community using fluorescent-surface antibodies. In all cases V. cholerae was able to grow and constituted around 10% of the final total cell concentration of the community. No significant effect of temperature was observed on the outcome of the competition. Mathematical modelling of the competition at the different temperatures based on the calculated [[micro].sub.max] values confirmed these experimental observations. The results demonstrate that V. cholerae is not only able to survive, but also able to grow in freshwater samples. In these experiments the bacterium was able to use a large fraction (12-62 %) of the [AOC.sub.app] available to the bacterial AOC-test community, indicating that V. cholerae has the ability to gain access to the substrates present in freshwater even in competition with an autochthonous bacterial lake water consortium.