ABSTRACT
Adequate consumption of fiber has a positive effect on health. The crossover study examined the effect of a pectin-enriched smoothie on gut microbiota and health parameters. During 3 weeks, 31 adults consumed two smoothies (11.6 or 4.8 g of fiber/day), alternating with washout periods in different order. At the end of each period, weekly food diaries, blood samples, and stool microbiota were collected. Changes in the microbiota during smoothie consumption were associated with baseline fiber intake. A greater proportion of up- (Lachnospira, Colidextribacter, and Bacteroides) or down-shifts (Streptococcus, Holdemanella) was observed in low-fiber (n = 22) compared to high-fiber consumers (n = 9). In both groups, the pectin-enriched smoothie reduced the number of the Ruminococcus torques group bacteria. Our results showed that the short-term approach is effective to estimate relationships between food components and gut bacteria.
ABSTRACT
The gut microbiota significantly contributes to human health and well-being. The aim of this study was to evaluate the stability and resilience of a consortium composed of three next-generation probiotics (NGPs) candidates originally found in the human gut. The growth patterns of Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Faecalibacterium prausnitzii were studied both individually and consortium. The growth kinetics of Akkermansia muciniphila (A. muciniphila), Bacteroides thetaiotaomicron (B. thetaiotaomicron), and Faecalibacterium prausnitzii (F. prausnitzii) were characterized both individually and in consortium using isothermal microcalorimetry and 16S ribosomal RNA next-generation sequencing. The consortium reached stability after three passages and demonstrated resilience to changes in its initial composition. The concentration of butyrate produced was nearly twice as high in the consortium compared to the monoculture of F. prausnitzii. The experimental conditions and methodologies used in this article are a solid foundation for developing further complex consortia.
Subject(s)
Calorimetry , Gastrointestinal Microbiome , RNA, Ribosomal, 16S , Humans , Gastrointestinal Microbiome/physiology , RNA, Ribosomal, 16S/genetics , Faecalibacterium prausnitzii/genetics , Akkermansia/growth & development , Akkermansia/physiology , Microbial Consortia/physiology , Microbial Consortia/genetics , High-Throughput Nucleotide Sequencing , Butyrates/metabolism , Probiotics , Verrucomicrobia/genetics , Verrucomicrobia/growth & development , Bacteroides/genetics , Bacteroides/growth & development , DNA, Bacterial/geneticsABSTRACT
Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.