Explore the vast range of titles available.

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.

Dysregulation of the gut microbiome is associated with several life-threatening conditions and thus might represent a useful target for the prevention of dementia. However, the relationship between the gut microbial population and dementia has not yet been fully clarified. We recruited outpatients visiting our memory clinic to participate in this study. Information on patient demographics, risk factors, and activities of daily living was collected, and cognitive function was assessed using neuropsychological tests and brain magnetic resonance imaging scans. Faecal samples were obtained, and the gut microbiome was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis, one of the most well-established and reliable 16S ribosomal RNA-based methods for classifying gut microbiota. Patients were divided into two groups, demented and non-demented. Multivariable logistic regression models were used to identify the variables independently associated with dementia. The T-RFLP analysis revealed differences in the composition of the gut microbiome: the number of Bacteroides (enterotype I) was lower and the number of ‘other’ bacteria (enterotype III) was higher in demented than non-demented patients. Multivariable analyses showed that the populations of enterotype I and enterotype III bacteria were strongly associated with dementia, independent of the traditional dementia biomarkers. Further studies of the metabolites of gut microbes are needed to determine the mechanism underlying this association.

Relationships between human gut microbiota, dietary habits, and health/diseases are the subject of epidemiological and clinical studies. However, the temporal stability and variability of the bacterial community in fecal samples remain unclear. In this study, middle-aged Japanese male and female volunteers (n = 5 each) without disease were recruited from the Sakura Diet Study. Fecal samples and lifestyle information were collected in every quarter and at each defecation for 7 continuous days. Next-generation sequencing of 16S rDNA and hierarchical clustering showed no time trend and intra-individual differences in both fecal sample sets. Significant inter-individual variations in seasonal and daily fecal sample sets were detected for 24 and 23 out of 39 selected dominant genera (>0.1 % of the total human gut microbiota; occupation rate >85 %), respectively. Intra- to inter-individual variance ratios in 26 and 35 genera were significantly <1.0 for seasonal and daily stabilities. Seasonal variation in fermented milk consumption might be associated with Bifidobacterium composition, but not with Lactobacillus. For most of the dominant genera in the human gut microbiota, inter-individual variations were significantly larger than intra-individual variations. Further studies are warranted to determine the contributions of human gut microbiota to nutritional metabolism, health promotion, and prevention/development of diseases.

Dysregulation of the gut microbiome is associated with dementia. However, the relationship between microbiome-associated metabolites and dementia has yet to be identified. Outpatients visiting a memory clinic in Japan enrolled in this cross-sectional study; 107 subjects were eligible for the study, 25 of which had dementia. We collected demographics, activities of daily living, risk factors, cognitive function, and brain imaging data. The gut microbiome was assessed using terminal restriction fragment length polymorphism analysis. Concentrations of faecal metabolite were measured. We used multivariable logistic regression analyses to identify whether metabolites were independently related to dementia. The concentrations of metabolites were significantly different between subjects with and those without dementia. Every 1 standard deviation increment in faecal ammonia concentration was associated with around a 1.6-fold risk for the presence of dementia. A higher faecal lactic acid concentration was related to a lower risk of dementia, by around 60%. A combination of higher faecal ammonia and lactic acid concentrations was indicative of the presence of dementia, and had a similar predictive value as traditional biomarkers of dementia. Thus, faecal ammonia and lactic acid are related to dementia, independently of the other risk factors for dementia and dysregulation of the gut microbiome.

Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. 14cWN4qpGoEHsF7NJvL5FB Video Abstract

This study aimed to investigate the gut microbial genera associated with skeletal muscle mass, using a large-scale survey from the standpoint of preventing sarcopenia. A total of 848 participants were included in the analysis. The mean (SD) ages of men (n = 353) and women (n = 495) were 50.0 (12.9) years and 50.8 (12.8) years, respectively. Body composition was assessed using appendicular skeletal muscle mass/body weight (ASM/BW), ASM, and BW. Additionally, the relationship between gut microbial genera and body composition was analyzed. The means (SD) of ASM/BW were 34.9 (2.4) % in men and 29.4 (2.9) % in women. Blautia and Bifidobacterium were positively associated with ASM/BW only in men (Blautia: β = 0.0003, Bifidobacterium: β = 0.0001). However, Blautia was negatively associated with BW (β = −0.0017). Eisenbergiella was positively associated with ASM/BW (β = 0.0209) and negatively associated with BW (β = −0.0769) only in women. Our results indicate that Blautia, Bifidobacterium and Eisenbergiella, which are positively associated with ASM/BW, might help increase skeletal muscle mass. ASM/BW may clarify the relationship between gut microbiota and skeletal muscle mass without being affected by obesity or excess body fat mass.

The gut microbiota has become a significant factor associated with health and disease. Although many studies have reported the implications of changes in the gut microbiota on cardiovascular diseases, there are no reports on the relationship between heart rate variability (HRV) and the gut microbiota. Therefore, we investigated the association between gut microbiota abundance and HRV parameters in this cross-sectional study of the general Japanese population. This study included 950 participants of the Iwaki Health Promotion Project who underwent a medical examination in 2019 that included HRV and gut microbiota measurements. At the genus level, multivariate regression analysis showed that higher gut microbial diversity was associated with a higher standard deviation of RR intervals (SDNN). Moreover, a higher SDNN was associated with a higher relative count of Lachnospiraceae incertae sedis. L. incertae sedis abundance was associated with higher HRV parameters such as SDNN, coefficient of variation of RR intervals, low-frequency component power (LF)/high-frequency component power, and LF. In the general Japanese population, higher gut microbial diversity and L. incertae sedis abundance were associated with higher HRV parameters.

Recent studies have revealed an association between the dysregulation of the gut microbiome and dementia. However, whether this dysregulation is associated with mild cognitive impairment (MCI), an early stage of cognitive decline, in patients without dementia remains unclear. We performed a cross-sectional analysis to determine the association between the gut microbiome and MCI. Data, including patient demographics, risk factors, cognitive function, and brain imaging, were collected. The gut microbiome was assessed through terminal restriction fragment length polymorphism analysis. Multivariable logistic regression models were used to identify factors independently associated with MCI. Graphical modelling was used to illustrate mutual associations between MCI and identified factors. We analysed 82 patients, 61 of whom exhibited MCI. Patients with MCI had a higher prevalence of Bacteroides . Furthermore, patients with more Bacteroides were more likely to present with white matter hyperintensity and high voxel-based specific regional analysis system for Alzheimer’s Disease (VSRAD) scores, indicating cortical and hippocampal atrophy. A multivariable logistic regression analysis revealed that a greater prevalence of Bacteroides was independently associated with MCI. Graphical modelling also showed a close association between Bacteroides and MCI. In conclusion, an increased prevalence of Bacteroides is independently associated with the presence of MCI in patients without dementia.

This study examined the effect of an exercise intervention on the composition of the intestinal microbiota in healthy elderly women. Thirty-two sedentary women that were aged 65 years and older participated in a 12-week, non-randomized comparative trial. The subjects were allocated to two groups receiving different exercise interventions, trunk muscle training (TM), or aerobic exercise training (AE). AE included brisk walking, i.e., at an intensity of ≥ 3 metabolic equivalents (METs). The composition of the intestinal microbiota in fecal samples was determined before and after the training period. We also assessed the daily physical activity using an accelerometer, trunk muscle strength by the modified Kraus–Weber (K-W) test, and cardiorespiratory fitness by a 6-min. walk test (6MWT). K-W test scores and distance achieved during the 6MWT (6MWD) improved in both groups. The relative abundance of intestinal Bacteroides only significantly increased in the AE group, particularly in subjects showing increases in the time spent in brisk walking. Overall, the increases in intestinal Bacteroides following the exercise intervention were associated with increases in 6MWD. In conclusion, aerobic exercise training that targets an increase of the time spent in brisk walking may increase intestinal Bacteroides in association with improved cardiorespiratory fitness in healthy elderly women.