scholarly journals The Impact of a Dynamic Working Environment on Human Gut Microbiota

2021 ◽  
Author(s):  
Lu Ling ◽  
Jun Zhou ◽  
Qianlong Meng ◽  
Ziran Zhang ◽  
Wenkun Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Clinical Characteristics ◽  
Dietary Habits ◽  
Living Environment ◽  
Working Environment ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Train Drivers ◽  
The Impact

Gut microbiota dysbiosis is associated with a variety of diseases, such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), metabolic diseases, allergic diseases, neurodevelopmental disorders and cancer. The human gut microbiota can be influenced by a variety of factors, including geography, dietary habits, living environment, age and altered lifestyle etc. This study was conducted to explore the gut microbiota compositions in officials who are in a stable working environment and train drivers who are in a dynamic working environment. Microbiota communities in the feces of 80 officials and 88 train drivers were analyzed using Illumina MiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene and ITS1 region of fungi. There were significant differences between the two groups in diversity and richness of gut microbiota, while the microbial community compositions of the two groups were similar. The relationship between gut microbiota and clinical characteristics was investigated. We found that more bacteria and fungi were positively correlated with clinical characteristics. Functional prediction analysis of the gut microbiota between the two groups by PICRUSt2 revealed significant differences between the official group and the train driver group. Elucidating these differences of the microbiome between the two groups will provide a foundation understanding of the impact of a dynamic environment on gut microbiota.

scholarly journals Considerations for the design and conduct of human gut microbiota intervention studies relating to foods

2020 ◽  
Vol 59 (8) ◽  
pp. 3347-3368
Author(s):  
J. R. Swann ◽  
M. Rajilic-Stojanovic ◽  
A. Salonen ◽  
O. Sakwinska ◽  
C. Gill ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Intervention Studies ◽  
Health Claims ◽  
Host Responses ◽  
Human Gut ◽  
Eligibility Criteria ◽  
Functional Changes ◽  
Human Gut Microbiota ◽  
The Impact

AbstractWith the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota–host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.

scholarly journals Optimisation of sample storage and DNA extraction for human gut microbiota studies​

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiota ◽  
Dna Extraction ◽  
Personalised Medicine ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Reliable Solution

Abstract Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Human gut microbiota – its diversity and impact on our health

2021 ◽  
pp. 71-100
Author(s):  
Sebastian Wardak
Keyword(s):  
Gut Microbiota ◽  
Short Chain Fatty Acids ◽  
Living Environment ◽  
Socioeconomic Conditions ◽  
Human Gut ◽  
Modern Molecular Biology ◽  
Rapid Changes ◽  
Human Digestive Tract ◽  
The Impact ◽  
Generation Sequencing

The human digestive tract is the living environment for billions of cells of various microorganisms that are part of the human microflora. The use of modern molecular biology techniques, such as NGS (Next Generation Sequencing), made it possible to study the microorganisms inhabiting the intestines and to understand their impact on human health. The gut microbiota plays a significant role in the synthesis and metabolism of many nutrients and metabolites, including short-chain fatty acids (SCFA), amino acids, lipids, bile acids and vitamins. Many factors such as diet, age, climate, and socioeconomic conditions influence the diversity of the microbiota. Rapid changes in the composition of the microbiota (disturbance of homeostasis) can lead to dysbiosis - a condition associated not only with intestinal disorders, but also with numerous extraintestinal diseases. The present work is a review of current reports on: research techniques used to analyze microbiota, the impact of various factors on its diversity and the impact of microbiota on our health.

scholarly journals Half-Elemental Diet Shifts the Human Intestinal Bacterial Compositions and Metabolites: A Pilot Study with Healthy Individuals

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jun Miyoshi ◽  
Daisuke Saito ◽  
Mio Nakamura ◽  
Miki Miura ◽  
Tatsuya Mitsui ◽  
...  
Keyword(s):  
Pilot Study ◽  
Gut Microbiota ◽  
Dietary Habits ◽  
Elemental Diet ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
The Impact ◽  
Time Point

Background and Aim. Half-elemental diet (ED) (900 kcal/day of ED) has clinical efficacy to treat Crohn’s disease (CD). However, the underlying mechanisms of how the ED exerts its efficacy remain unclear. Alterations of the gut microbiota, known as dysbiosis, have been reported to play a role in CD pathogenesis. Many variables including diet affect the gut microbiota. We hypothesized that half-ED has the potential to change the gut microbiota composition and functions leading to anti-inflammatory actions. Given that inflammation can be a confounding factor affecting the intestinal microbiota, we aimed to test our hypothesis among healthy individuals in this pilot study. Methods. This prospective study included four healthy volunteers. The subjects continued their dietary habits for 2 weeks after the registration of the study and then started half-ED replacing 900 kcal of the regular diet with ED (time point 1, T1). The subjects continued half-ED for 2 weeks (T2). After the withdrawal of ED, subjects resumed their original dietary habits for 2 weeks (T3). Fecal samples were collected from all subjects at all time points, T1-3. Fecal DNA and metabolites were extracted from the samples. We performed 16S rRNA gene amplicon sequencing and metabolomic analysis to examine the bacterial compositions and intestinal metabolites. Results. There were differences in the gut bacterial compositions and metabolites at each time point as well as overtime changing patterns between subjects. Several bacteria and metabolites including short-chain fatty acids and bile acids altered significantly across the subjects. The bacterial membership and intestinal metabolites at T3 were different from T1 in all subjects. Conclusions. Half-ED shifts the gut bacterial compositions and metabolites. The changes varied with each individual, while some microbes and metabolites change commonly across individuals. The impact of half-ED may persist even after the withdrawal. This trial is registered with UMIN ID: 000031920.

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

PROTEOMICS ◽  
2015 ◽  
Vol 15 (20) ◽  
pp. 3474-3485 ◽  
Author(s):  
Alessandro Tanca ◽  
Antonio Palomba ◽  
Salvatore Pisanu ◽  
Maria Filippa Addis ◽  
Sergio Uzzau
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
The Impact

Understanding the impact of chia seed mucilage on human gut microbiota by using the dynamic gastrointestinal model simgi®

2018 ◽  
Vol 50 ◽  
pp. 104-111 ◽  
Author(s):  
Alba Tamargo ◽  
Carolina Cueva ◽  
Laura Laguna ◽  
M.Victoria Moreno-Arribas ◽  
Loreto A. Muñoz
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Chia Seed ◽  
The Impact ◽  
Seed Mucilage

scholarly journals Production of conjugated linoleic acid (CLA): effect of inulin on microbial composition and CLA concentration in a human intestinal model

2020 ◽  
Vol 79 (OCE2) ◽  
Author(s):  
Ilaria Carafa ◽  
Domenico Masuero ◽  
Urska Vrhovsek ◽  
Giovanni Bittante ◽  
Elena Franciosi ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Illumina Miseq ◽  
Ultra Performance Liquid Chromatography ◽  
Rrna Gene ◽  
Human Gut ◽  
Microbial Composition ◽  
Human Gut Microbiota

AbstractConjugated linoleic acids (CLAs) show a number of putative health-promoting activities including anti-carcinogenic, anti-adipogenic, anti-diabetogenic, anti-inflammatory and antioxidant actions. CLAs are naturally produced by ruminal bacteria and several studies demonstrate that various lactobacilli and bifidobacteria are also able to produce CLAs in vitro from linoleic acid (LA). However, the ability of the human gut microbiota to produce CLA is less extensively studied. Our hypothesis is that the human gut microbiota is able to convert LA to CLA, and that the readily fermentable fiber inulin would positively modulate the growth of CLA-producing bacteria and, consequently increase the CLA content in the intestine.The capability of the faecal microbiota from five healthy donors to produce CLA was tested in anaerobic batch cultures for 48 hours at pH 5.5 and 6.5. Test treatments were linoleic acid (LA; 1 mg/mL) + bovine serum albumin (BSA; 0.2 mg/mL), and LA (1 mg/mL) + BSA (0.2 mg/mL) + inulin (1%, w/v) compared to a control BSA (0.2 mg/mL) fermentation. The microbial composition was analyzed 0, 24 and 48 hours after starting the fermentation by 16S rRNA gene Illumina MiSeq sequencing (V3-V4 region). CLAs were quantified by Ultra performance liquid chromatography - tandem mass spectrometer (UPLC-MS/MS) and bi-dimensional gas chromatography (GC x GC).The inclusion of LA + BSA + inulin at pH 5.5 significantly increased the relative abundance of Collinsella aerofaciens (p < 0.05), and tended to increase the relative abundance of bifidobacteria. LA + BSA + inulin at both pH 5.5 and 6.5 reduced the relative abundance of Parabacteroides, Bilophila, Clostridia and Enterobacteriaceae (p < 0.05). The concentration of CLA, in particular the isomer cis9,trans11 C18:2, was significantly higher in the LA + BSA + inulin group at pH 5.5 after 24 and 48 hours fermentation.The data show that the treatment LA + BSA + inulin at pH 5.5 induce substantial changes in microbiota composition, including bifidogenesis and CLA production in a human intestinal microbiota model. The changes of relative abundance detected are consistent with changes in gut bacteria previously linked to human health. Collinsella aerofaciens has been reported for reducing bloating, in particular in subjects suffering from irritable bowel syndrome, while Clostridia, Bilophila and Enterobacteriaceae causes human infections. In addition, the increase of bifidobacteria and LAB, which have previously been shown in vitro to produce CLA, may also be involved in CLA production under simulated cecal microbiome. These preclinical observations warrant confirmation in suitably designed animal and human mechanistic studies.

scholarly journals An extended reconstruction of human gut microbiota metabolism of dietary compounds

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Telmo Blasco ◽  
Sergio Pérez-Burillo ◽  
Francesco Balzerani ◽  
Daniel Hinojosa-Nogueira ◽  
Alberto Lerma-Aguilera ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Metabolic Networks ◽  
16S Rrna Gene Sequencing ◽  
Complex Problem ◽  
Rrna Gene ◽  
Limited Information ◽  
Sequencing Data ◽  
Human Gut ◽  
Human Gut Microbiota

AbstractUnderstanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.

scholarly journals Ramadan Fasting Leads to Shifts in Human Gut Microbiota Structured by Dietary Composition

2021 ◽  
Vol 12 ◽  
Author(s):  
Ikram Ali ◽  
Ke Liu ◽  
Danfeng Long ◽  
Shah Faisal ◽  
Mian Gul Hilal ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Ethnic Groups ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Dietary Composition ◽  
Human Gut ◽  
Ramadan Fasting ◽  
Human Gut Microbiota ◽  
Before And After ◽  
Chinese Group

The structure and diversity of human gut microbiota are directly related to diet, though less is known about the influences of ethnicity and diet-related behaviors, such as fasting (intermittent caloric restriction). In this study, we investigated whether fasting for Ramadan altered the microbiota in Chinese and Pakistani individuals. Using high-throughput 16S rRNA gene sequencing and self-reported dietary intake surveys, we determined that both the microbiota and dietary composition were significantly different with little overlap between ethnic groups. Principal Coordinate Analyses (PCoA) comparison of samples collected from both groups before and after fasting showed partial separation of microbiota related to fasting in the Pakistani group, but not in the Chinese group. Measurement of alpha diversity showed that Ramadan fasting significantly altered the coverage and ACE indices among Chinese subjects, but otherwise incurred no changes among either group. Specifically, Prevotella and Faecalibacterium drove predominance of Bacteroidetes and Firmicutes in the Pakistani group, while Bacteroides (phylum Bacteroidetes) were the most prevalent among Chinese participants both before and after fasting. We observed significant enrichment of some specific taxa and depletion of others in individuals of both populations, suggesting that fasting could affect beta diversity. Notably, Dorea, Klebsiella, and Faecalibacterium were more abundant in the Chinese group after fasting, while Sutterella, Parabacteroides, and Alistipes were significantly enriched after fasting in the Pakistani group. Evaluation of the combined groups showed that genera Coprococcus, Clostridium_XlV, and Lachnospiracea were all significantly decreased after fasting. Analysis of food intake and macronutrient energy sources showed that fat-derived energy was positively associated with Oscillibacter and Prevotella, but negatively associated with Bacteroides. In addition, the consumption of sweets was significantly positively correlated with the prevalence of Akkermansia. Our study indicated that diet was the most significant influence on microbiota, and correlated with ethnic groups, while fasting led to enrichment of specific bacterial taxa in some individuals. Given the dearth of understanding about the impacts of fasting on microbiota, our results provide valuable inroads for future study aimed at novel, personalized, behavior-based treatments targeting specific gut microbes for prevention or treatment of digestive disorders.

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