Self-Initiated Dietary Adjustments Alter Microbiota Abundances: Implications for Perceived Health.

Personalized and self-initiated dietary adjustments have been shown to alleviate mental and somatic complaints. Here, we investigated the potential role of gut microbiome alterations underlying these effects. For this purpose, participants (n = 185) underwent a four-week self-initiated dietary intervention and filled out weekly questionnaires on their dietary intake, somatic and mental symptoms, and physical activity.

GUT MICROBIOME DIVERSITY OF THREE RHINOCEROS SPECIES IN EUROPEAN ZOOS.

The wild rhinoceros populations have declined drastically in the past decades because the rhinoceros are heavily hunted for their horns. Zoological institutions aim to conserve rhinoceros populations in captivity, but one of the challenges of conservation is to provide food sources that resemble those available in the wild. Considering that the mammalian gut microbiota is a pivotal player in their host's health, the gut microbiota of rhinoceros may also play a role in the bioavailability of nutrients.

Development of a reproducible small intestinal microbiota model and its integration into the SHIME-system, a dynamic gut model.

The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region . This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME-technology.

Screen the unforeseen: Microbiome-profiling for detection of zoonotic pathogens in wild rats.

Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed.

Anxiolytic effects of a galacto-oligosaccharides prebiotic in healthy females (18-25 years) with corresponding changes in gut bacterial composition.

Current research implicates pre- and probiotic supplementation as a potential tool for improving symptomology in physical and mental ailments, which makes it an attractive concept for clinicians and consumers alike. Here we focus on the transitional period of late adolescence and early adulthood during which effective interventions, such as nutritional supplementation to influence the gut microbiota, have the potential to offset health-related costs in later life. We examined multiple indices of mood and well-being in 64 healthy females in a 4-week double blind, placebo controlled galacto-oligosaccharides (GOS) prebiotic supplement intervention and obtained stool samples at baseline and follow-up for gut microbiota sequencing and analyses.

On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications.

Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Correspondingly, commercial interest has risen for applications where microbial communities make important contributions. These include food production, probiotics, cosmetics, and enzyme discovery.

Novel sequencing technologies to support industrial biotechnology.

Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and processing to bio-based chemicals, biofuels and pharmaceutical products. Next generation DNA sequencing technologies play an increasingly important role in improving and accelerating microbial strain development for existing and novel bio-products via screening, gene and pathway discovery, metabolic engineering and additional optimization and understanding of large-scale manufacturing. In this mini-review, we describe novel DNA sequencing and analysis technologies with a focus on applications to industrial strain development, enzyme discovery and microbial community analysis.

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints.

The general consensus is that the abundance of tap water bacteria is greatly influenced by water purification and distribution. Those bacteria that are released from biofilm in the distribution system are especially considered as the major potential risk for drinking water bio-safety. For the first time, this full-scale study has captured and identified the proportional contribution of the source water, treated water, and distribution system in shaping the tap water bacterial community based on their microbial community fingerprints using the Bayesian "SourceTracker" method.

The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows.

DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100).

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen.

Diurnal patterns of ruminal fermentation metabolites and microbial communities are not commonly assessed when investigating variation in ruminal CH production. The aims of this study were to monitor diurnal patterns of: (i) gaseous and dissolved metabolite concentrations in the bovine rumen, (ii) H and CH emitted, and (iii) the rumen microbiota. Furthermore, the effect of dietary inclusion of linseed oil on these patterns was assessed.

Effects of pectin supplementation on the fermentation patterns of different structural carbohydrates in rats.

Scope: We aimed to investigate and compare the effects of four types of pectins on dietary fiber (DF) fermentation, microbiota composition, and short chain fatty acid (SCFA) production throughout the large intestine in rats.

Methods And Results: Male Wistar rats were given diets supplemented with or without 3% structurally different pectins for 7 weeks. Different fermentation patterns of pectins and different location of fermentation of pectin and diet arabinoxylans (AXs) in the large intestine were observed.

T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut.

Dysbiosis of the intestinal microbial community is considered a risk factor for development of chronic intestinal inflammation as well as other diseases such as diabetes, obesity and even cancer. Study of the innate and adaptive immune pathways controlling bacterial colonization has however proven difficult in rodents, considering the extensive cross-talk between bacteria and innate and adaptive immunity. Here, we used the zebrafish to study innate and adaptive immune processes controlling the microbial community.

Immunomodulatory properties of Streptococcus and Veillonella isolates from the human small intestine microbiota.

The human small intestine is a key site for interactions between the intestinal microbiota and the mucosal immune system. Here we investigated the immunomodulatory properties of representative species of commonly dominant small-intestinal microbial communities, including six streptococcal strains (four Streptococcus salivarius, one S. equinus, one S.

The small intestine microbiota, nutritional modulation and relevance for health.

The intestinal microbiota plays a profound role in human health and extensive research has been dedicated to identify microbiota aberrations that are associated with disease. Most of this work has been targeting the large intestine and fecal microbiota, while the small intestine microbiota may also have a profound impact on various aspects of the host's physiology, including immune, metabolic and endocrine functions. This review highlights the recent advances made in the study of the human small intestine microbiota.

Aberrant gut microbiota composition at the onset of type 1 diabetes in young children.

Aims/hypothesis: Recent studies indicate that an aberrant gut microbiota is associated with the development of type 1 diabetes, yet little is known about the microbiota in children who have diabetes at an early age. To this end, the microbiota of children aged 1-5 years with new-onset type 1 diabetes was compared with the microbiota of age-matched healthy controls.

Methods: A deep global analysis of the gut microbiota composition was established by phylogenetic microarray analysis using a Human Intestinal Tract Chip (HITChip).

Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S.

Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine.

Enterococcus sp. strain HSIEG1 was isolated from the human small intestine. Its draft genome predicts a broad carbohydrate fermentation capability, which matches well with the observed physiological characteristics of this strain.

Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.

Veillonella species are frequently encountered commensals in the human small intestine. Here, we report the draft genome sequence of the first cultured representative from this ecosystem, Veillonella parvula strain HSIVP1. The genome is predicted to encode all the necessary enzymes required for the pathway involved in the conversion of lactate to propanoate.

Diversity of human small intestinal Streptococcus and Veillonella populations.

Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S.

Dietary heme alters microbiota and mucosa of mouse colon without functional changes in host-microbe cross-talk.

Colon cancer is a major cause of cancer deaths in Western countries and is associated with diets high in red meat. Heme, the iron-porphyrin pigment of red meat, induces cytotoxicity of gut contents which injures surface cells leading to compensatory hyperproliferation of crypt cells. This hyperproliferation results in epithelial hyperplasia which increases the risk of colon cancer.

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.

The human gastrointestinal tract (GI tract) harbors a complex community of microbes. The microbiota composition varies between different locations in the GI tract, but most studies focus on the fecal microbiota, and that inhabiting the colonic mucosa. Consequently, little is known about the microbiota at other parts of the GI tract, which is especially true for the small intestine because of its limited accessibility.

Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples.

Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results.