The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.

Bile acids are natural detergents that aid in the absorption of dietary lipids. Fatty acid binding protein 6 (Fabp6) is a component of the bile acid recovery system that operates in the small intestine. The aim of this study was to determine if Fabp6 deficiency causes dietary fat malabsorption. Wild‐type and Fabp6‐deficient mice were fed a Western‐style diet (WSD) or a reference low‐fat diet (LFD) for 10 weeks. The body weight gain, bile acid excretion, fat excretion, energy metabolism, and major gut microbial phyla of the mice were assessed at the end of the controlled diet period. Fabp6−/− mice exhibited enhanced excretion of both bile acids and fat on the WSD but not on the LFD diet. Paradoxically, male Fabp6−/− mice, but not female Fabp6−/− mice, had greater adiposity despite increased fat excretion. Analysis of energy intake and of expenditure by indirect calorimetry revealed sex differences in physical activity level and respiratory quotient, but these did not account for the enhanced adiposity displayed by male Fabp6−/− mice. Analysis of stool DNA showed sex‐specific changes in the abundance of major phyla of bacteria in response to Fabp6 deficiency and WSD feeding. The results obtained indicate that the malabsorption of bile acids that occurs in Fabp6−/− mice is associated with dietary fat malabsorption on the high‐fat diet but not on the low‐fat diet. The WSD induced a sexually dimorphic increase in adiposity displayed by Fabp6−/− mice and sexually distinct pattern of change in gut microbiota composition.

Nanocapsules of alpha‐linolenic acid (α‐LA) were prepared by a modified emulsion diffusion technique with encapsulation efficiency of 93%. Polylactic acid (PLA) was used as the encapsulating polymer with acetone and ethyl acetate as organic solvents, and Tween 20, gelatin and Pluronic‐F68 in water as stabilizers. Two ratios of organic to aqueous phases were used with each solvent and stabilizer. Nanocapsule dispersions with a particle size less than 100 nm and a zeta potential as high as 33 mV were obtained as verified by scanning electron microscopy and the dynamic light scattering technique respectively. Both particle size and zeta potential were influenced by such preparation conditions as the type of stabilizer, type of organic solvent and the organic to aqueous phase ratio. Acetone was superior to ethyl acetate, and Tween 20 was superior to each of Pluronic‐F68 and gelatin in obtaining smaller, less aggregated nanocapsules. An organic to aqueous phase ratio of 1:5 was shown to be more suitable for the formation of smaller nanocapsules, particularly when acetone was used as the organic solvent.

In vitro gut model systems permit the growth of gut microbes outside their natural habitat and are essential to the study of gut microbiota. Systems available today are limited by a lack of scalability and flexibility in the mode of operation. Here, we describe the development of a versatile bioreactor module that can be easily adjusted for culture size and capable of sensing and controlling of environmental parameters such as pH control of culture medium, rate of influx and efflux of the culture medium, and aerobic/anaerobic atmosphere. Bioreactor modules can be operated as single units or linked in series to construct a model of a digestive tract with multiple compartments to allow the growth of microbiota in vitro. We tested the growth of synthetic and natural bacterial communities in a multicompartment continuous dynamic culture model simulation of the mammalian gut. The distal compartments of a sterile system inoculated with the synthetic bacterial community at the proximal module attained a stable bacterial density by 24 h, and all the genera present in the inoculum were firmly established in the distal modules simulating the large intestine at 5 days of continuous culture. A natural bacterial community simultaneously inoculated into the distal modules attained a stable bacterial composition at the phylum level by Day 7 of continuous culture. The findings illustrate the utility of the system to culture mixed bacterial communities which can be used to study the collective biological activities of the cultured microbiota in the absence of host influence.

In vitro gut model systems permit the growth of gut microbes outside their natural habitat and are essential to the study of gut microbiota. Systems available today are limited by lack of scalability and flexibility in mode of operation. Here we describe the development of a versatile bioreactor module capable of sensing and controlling of environmental parameters such as pH control of culture medium, rate of influx and efflux of the culture medium, and aerobic/anaerobic atmosphere. Modules can be linked in series to construct a model of a digestive tract to allow the growth of microbiota in vitro. We tested the growth of a model bacterial community in a simulated mammalian gut model. The model attained and maintained a stable bacterial community that metabolized bile acids. The findings illustrate the utility of the model to grow to culture a mixed bacterial community and recapitulate biological activities such as bile acid metabolism in vitro.