Alpha Diversity Measures Research Articles

Nylon microfibers develop a distinct plastisphere but have no apparent effects on the gut microbiome or gut tissue status in the blue mussel, Mytilus edulis.

Ingestion of microplastics (MP) by suspension-feeding bivalves has been well-documented. However, it is unclear whether exposure to MP could damage the stomach and digestive gland (gut) of these animals, causing ramifications for organism and ecosystem health. Here, we show no apparent effects of nylon microfiber (MF) ingestion on the gut microbiome or digestive tissues of the blue mussel, Mytilus edulis. We exposed mussels to two low concentrations (50 and 100 particles/L) of either nylon MF or Spartina spp. particles (dried, ground marsh grass), ca. 250-500 μm in length, or a no particle control laboratory treatment for 21 days. Results showed that nylon MF, when aged in coarsely filtered seawater, developed a different microbial community than Spartina spp. particles and seawater, however, even after exposure to this different community, mussel gut microbial communities resisted disturbance from nylon MF. The microbial communities of experimental mussels clustered together in ordination and were similar in taxonomic composition and measures of alpha diversity. Additionally, there was no evidence of damage to gut tissues after ingestion of nylon MF or Spartina spp. Post-ingestive particle processing likely mediated a short gut retention time of these relatively large particles, contributing to the negligible treatment effects.

Geographic social vulnerability is associated with the alpha diversity of the human microbiome.

The human microbiome ecosystems living within the human body are exposed to exogenous foreign substances from the various environments that humans live within. Therefore, dynamics between microbes and human hosts can be influenced by environmental changes, which potentially impact microbiome composition and diversity. Geographic area, as a microbiome-relevant environmental factor, has been well reported. Human geography, however, is often linked to socioeconomic status, racial and ethnic population enclaves, and disparities in area disadvantage. Potential mechanisms linking the microbiome to factors tied to area disadvantage include household crowding, use of public transportation, and lack of exposure to biodiverse natural environments. Through an analysis of data from the Human Microbiome Project including healthy adults who reported residential area information at the time of microbiome sampling (n = 201), we found a significant relationship between the social vulnerability index (SVI), as a measure of area disadvantage, and multiple alpha diversity measures across oral, airways, and urogenital sites when controlling for age, gender, and body mass index. With regard to race/ethnicity, we found significant mediation by SVI score to explain racial/ethnic differences in urogenital microbiome diversity in females. Our results highlight the importance of considering environmental variables such as area social vulnerability as a variable of interest in microbiome studies within healthy individuals and suggest a potential role to explain urogenital race/ethnicity differences. Future studies including a diverse, representative community-based population, more precise residential location, and inclusion of related risk factors such as dietary intake, are needed to further understand the implications of these results. IMPORTANCE As a risk factor for conditions related to the microbiome, understanding the role of SVI on microbiome diversity may assist in identifying public health implications for microbiome research. Here we found, using a sub-sample of the Human Microbiome Project phase 1 cohort, that SVI was linked to microbiome diversity across body sites and that SVI may influence race/ethnicity-based differences in diversity. Our findings, build on the current knowledge regarding the role of human geography in microbiome research, suggest that measures of geographic social vulnerability be considered as additional contextual factors when exploring microbiome alpha diversity.

Age-associated changes in intestinal health biomarkers in dogs.

The gut microbiome is critical for maintaining host health. In healthy humans, the aging process is one of the main factors modulating the changes in the intestinal microbiota. However, little is known about the relationship between gut health, microbiota, and the aging process in dogs. The present study aims to explore the differences in the intestinal microbiota and intestinal health based on fecal biomarkers in a population of dogs of different ages. The study involved 106 dogs of different breeds aged between 0.2 and 15 years categorized as senior (>7 years; n = 40), adult (2-7 years; n = 50), and junior (< 2 years; n = 16). Fecal samples were collected during the same period at the same facilities. The analysis included the following gut health indicators: 16S rRNA gene sequencing to investigate the differences in the fecal microbiota; qPCR to determine the dysbiosis index; fecal short-chain fatty acid concentrations; fecal calprotectin; and immunoglobulin A. Beta diversity analysis revealed a significant difference with a small effect size (p = 0.003; R = 0.087) among age categories based on the unweighted UniFrac metric, but no significance was observed based on the weighted UniFrac metric or Bray-Curtis distances. There were no significant differences in the alpha diversity measures or the fecal dysbiosis index among age categories. Senior dogs had significantly higher relative abundance proportions in phyla Bacteroidota and Pseudomonadota and the genus Faecalibacterium, but not on qPCR analysis. At the family level, Ruminococcaceae, Uncl. Clostridiales.1, Veillonellaceae, Prevotellaceae, Succinivibrionaceae, and Bacteroidaceae abundances were higher in the senior category than in the adult and/or junior categories. Relative proportions, but not concentrations of fecal acetate, were higher in the senior category, while butyrate, isovaleric acid, and valeric acid were lower. The valeric acid concentration was significantly lower in the senior category than in the adult category. Calprotectin and immunoglobulin A levels did not differ significantly across groups. In conclusion, this study observed multiple minor changes in the fecal microbiota composition and the relative amount of short-chain fatty acids in dogs among different age groups, but studies in larger populations representative of all ages are warranted to refine the present results.

Dietary alfalfa hay or lipid-soluble alfalfa extract may improve broiler growth, but fiber presence may be detrimental during Eimeria vaccine challenge

Lipid-soluble components in late-cutting alfalfa are linked to beneficial immune and microbiota responses in mouse challenge models; therefore, responses in a comparative poultry Eimeria challenge model were investigated. The study objective was to evaluate performance, immunity, and the cecal microbiota in broilers fed ground hay or lipid-soluble extract from late (fifth) cutting alfalfa during Eimeria challenge. At hatch, 432 Ross 708 broilers were placed in 24 floor pens (18 birds/pen) and assigned to 3 isocaloric/isonitrogenous dietary treatments consisting of control, 5% ground hay, or 0.25% lipid-soluble extract for a 42-d trial divided into 14 d starter, grower, and finisher periods. On d 14, 4 birds/treatment were euthanized to collect blood and cecal contents before half the remainder were inoculated with 10X Merck Coccivac-B52 (Kenilworth, NJ). Tissue samples were collected at 3, 7, 14, and 28 d postinoculation (pi; 4 birds/diet×Eimeria group) with body weight (BW) and feed intake (FI) recorded weekly. Immune populations within peripheral blood mononuclear cells were characterized by flow cytometry while cecal microbial communities were profiled by 16S rRNA gene amplicon sequencing. Data were normalized when appropriate and analyzed to evaluate the effects of diet, Eimeria challenge, and timepoint (SAS 9.4; P ≤ 0.05). Before challenge, dietary alfalfa hay or extract increased FI 6.9 to 8.0% and increased CD3+ T cells 19.3 to 24.9% compared to control-fed birds (P ≤ 0.007). Alfalfa did not significantly affect post-Eimeria performance, but Eimeria-challenged birds fed hay showed the greatest numeric reduction in final BW compared to their unchallenged counterparts (0.17 kg) vs. control and extract-fed birds (0.02-0.04 kg). Immune cell changes did not indicate recruitment from peripheral blood to local infection sites; however, alfalfa hay may have accelerated Bu-1+ B cell development by 7 d in unchallenged birds (P < 0.0001). During Eimeria-challenge, dietary alfalfa extract preserved alpha diversity measures related to species richness (P ≤ 0.007). Collectively, these results indicate potential benefits of feeding lipid-soluble extract from late cutting alfalfa to broilers during Eimeria challenge.

Prenatal lead exposure is negatively associated with the gut microbiome in childhood.

Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood. This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old. Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders. Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6 (SE = 2.1) ug/L and 34.9 (SE = 2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ = -0.17, 95%CI = [-0.46,0.11]; 3Tβ = -0.17, 95%CI = [-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure. Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.

1143-P: Elevated Serum IgA and the Gut Microbiome in Pediatric Type 1 Diabetes (T1D)

Elevated serum IgA occurs in ~20% of children with new onset T1D, although its potential role in T1D pathogenesis is not understood. Gut dysbiosis is present at onset of T1D and is strongly associated with its pathogenesis. Mucosal IgA is well known to influence the microbiome and vice versa. In animal models, serum IgA responds to microbiome changes, thereby inducing a protective response to gut invasion by pathogens. However, the relationship between gut microbiome and serum IgA in humans with T1D is unknown. Thus, we aimed to assess if elevated serum IgA is associated with gut dysbiosis at T1D onset. We enrolled 47 children between 7/2021 and 9/2022: New onset T1D with elevated serum IgA (T1D-Hi-IgA, n=14), new onset T1D with normal serum IgA (T1D-Nl-IgA, n=18) and controls (siblings of new onset T1D, n=15). Exclusions: &amp;lt;2 yrs age; antibiotics; probiotics; inflammatory bowel disease; celiac disease; or acute illness &amp;lt;10 days of stool collection. Demographic and clinical variables, diet questionnaires and stool were collected. Stool microbiome was determined via 16Sv4 rDNA sequencing. Differences in alpha and beta diversity along with taxa abundance were assessed. We found that the relative abundance of members of families Oscillospiraceae and Lachnospiraceae, both of which contain butyrate producers, were significantly associated with elevated IgA irrespective of T1D status (p&amp;lt;0.05); higher in T1D-Hi-IgA vs T1D-Nl-IgA (p&amp;lt;0.05); yet similar in T1D-Hi-IgA vs controls. Measures of alpha diversity, including richness and evenness, were also increased in T1D-Hi-IgA vs T1D-Nl-IgA, though these differences did not reach significance (richness: p=0.074; evenness: p=0.135). Similar results were observed for beta diversity. In sum, in children with new onset T1D, elevated serum IgA is associated with beneficial microbial taxa such as butyrate producers, with a trend towards increased diversity, similar to healthy siblings. Further studies are needed to understand its involvement in T1D pathogenesis. Disclosure A.Thakkar: None. M.J.Redondo: None. J.Hajjar: None. J.Petrosino: None. K.L.Hoffman: Consultant; Cooper Surgical. J.Cormier: None. M.Ahmed: None. X.C.Huang: None.

Half a century of herb layer changes in Quercus-dominated forests of the Western Carpathians

Species composition of European temperate Quercus forests have undergone dramatic changes in the past century. Observed changes have largely been attributed to anthropogenic environmental changes that drove the processes of thermophilization, eutrophication, or biotic homogenization. However, ecological processes behind these changes can be difficult to explain considering the variability among regions: their history, management, landscape patterns, site properties, and vegetation types. To reveal vegetation change trends and their drivers in the subcontinental Western Carpathians, we analysed vegetation and environmental data from 158 quasi-permanent plots established between 1961 and 1980 in Quercus petraea- dominated forests on the andesite bedrock of the Slovenské stredohorie Mountains in Slovakia (Central Europe), and we resurveyed them again between 2005 and 2020.Among alpha and gamma diversity measures, we found only slight species richness decreases. A significant shift in species composition associated with very high species turnover (64%) and a decrease in herb layer cover (by 24%) resulted in higher spatial heterogeneity of herb understoreys in the resurvey. Winning species were more thermophilous, eutrophic, and mesic/oceanic plants of lower latitudes, replacing original species of open Quercus forests. Increased temperatures was the most significant environmental driver. Climate warming corresponded not only to thermophilization, but, after interaction with management, it was also related to eutrophication of the herb layer. Eutrophication was identified as the main trend of the species composition changes (mean EIV for nutrients of winners was 5.9 compared to 4.1 of losers) even though the effect of anthropic nitrogen depositions was negligible. Successive undergrowing of Quercus canopies by more shade-casting trees (Acer campestre, Carpinus betulus, and Fagus sylvatica) in the period of decreasing management intensity was another major driver. Their increase by 8.6% in the resurveyed plots contributed to decreased species richness and they supported shade-tolerant eutrophic understorey species typical of mesic Carpinus betulus and Fagus sylvatica forests.We concluded that Quercus forests in the Western Carpathians underwent thermophilization and eutrophication, similar to the forests in densely inhabited Western Europe; however, their plant understoreys were not homogenized, and eutrophication was not driven by nitrogen depositions. Eutrophication should be recognised as the next important negative impact of global warming on ecosystems. Dramatic changes in species composition and loss of original characteristic species can only be partly halted by reducing shade-casting trees from lower tree layers in managed stands.

Effects of exercise and physical activity on gut microbiota composition and function in older adults: a systematic review

BackgroundThe characterization and research around the gut microbiome in older people emphasize microbial populations change considerably by losing the diversity of species. Then, this review aims to determine if there is any effect on the gut microbiota of adults older than 65 that starts an exercise intervention or improves physical activity level. Also, this review describes the changes in composition, diversity, and function of the gut microbiota of older subjects that had improved their physical activity level.MethodsThe type of studies included in this review were studies describing human gut microbiota responses to any exercise stimulus; cross-sectional studies focused on comparing gut microbiota in older adults with different physical activity levels—from athletes to inactive individuals; studies containing older people (women and men), and studies written in English. This review's primary outcomes of interest were gut microbiota abundance and diversity.ResultsTwelve cross-sectional studies and three randomized controlled trials were examined. Independently of the type of study, diversity metrics from Alpha and Beta diversity remained without changes in almost all the studies. Likewise, cross-sectional studies do not reflect significant changes in gut microbiota diversity; no significant differences were detected among diverse groups in the relative abundances of the major phyla or alpha diversity measures. Otherwise, relative abundance analysis showed a significant change in older adults who conducted an exercise program for five weeks or more at the genus level.ConclusionsHere, we did not identify significant shifts in diversity metrics; only one study reported a significant difference in Alpha diversity from overweight people with higher physical activity levels. The abundance of some bacteria is higher in aged people, after an exercise program, or in comparison with control groups, especially at the genus and species levels. There needs to be more information related to function and metabolic pathways that can be crucial to understand the effect of exercise and physical activity in older adults.Trial registrationPROSPERO ID: CRD42022331551.

Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.

Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 yr; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (N = 18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment × transport were tested, with P < 0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet × transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.

Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs

The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC–MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH4) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH4 on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.

Evaluation of alcohol-free mouthwash for studies of the oral microbiome.

Oral bacteria play important roles in human health and disease. Oral samples collected using ethanol-containing mouthwash are widely used for oral microbiome studies. However, ethanol is flammable and not ideal for transportation/storage in large quantities, and some individuals may avoid ethanol due to the burning sensation or due to various personal, medical, religious, and/or cultural factors. Here, we compared ethanol-free and ethanol-containing mouthwashes using multiple microbiome metrics and assessed the stability of the mouthwash samples stored up to 10 days before processing. Forty volunteers provided oral wash samples collected using ethanol-free and ethanol-containing mouthwashes. From each sample, one aliquot was immediately frozen, one was stored at 4°C for 5 days and frozen, while the third aliquot was stored for 5 days at 4°C and 5 days at ambient temperature to mimic shipping delays and then frozen. DNA was extracted, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatic processing was performed using QIIME 2. Microbiome metrics measured in the two mouthwash types were very similar, with intraclass correlation coefficients (ICCs) for alpha and beta diversity metrics greater than 0.85. Relative abundances of some taxa were significantly different, but ICCs of the top four most abundant phyla and genera were high (> 0.75) for the comparability of the mouthwashes. Stability during delayed processing was also high for both mouthwashes based on alpha and beta diversity measures and relative abundances of the top four phyla and genera (ICCs ≥ 0.90). These results demonstrate ethanol-free mouthwash performs similarly to ethanol-containing mouthwash for microbial analyses, and both mouthwashes are stable for at least 10 days without freezing prior to laboratory processing. Ethanol-free mouthwash is suitable for collecting and shipping oral wash samples, and these results have important implications for planning future epidemiologic studies of the oral microbiome.

Microbial community succession in the intestine of mice with deep partial-thickness burns.

Burn injury has been shown to lead to changes in the composition of the gut microbiome and cause other damage in patients. However, little is known about how the gut microbial community evolves in individuals who have recovered from burn injury. In this study, we established a model of deep partial-thickness burn in mice and collected fecal samples at eight time points (pre-burn, 1, 3, 5, 7, 14, 21, and 28 days post-burn) for 16S rRNA amplification and high-throughput sequencing. The results of the sequencing were analyzed using measures of alpha diversity, and beta diversity and taxonomy. We observed that the richness of the gut microbiome declined from day 7 post-burn and that the principal component and microbial community structure varied over time. On day 28 after the burn, the microbiome composition largely returned to the pre-burn level, although day 5 was a turning point for change. Some probiotics, such as the Lachnospiraceae_NK4A136_group, decreased in composition after the burn but were restored in the later recovery period. In contrast, Proteobacteria showed an opposite trend, which is known to include potential pathogenic bacteria. These findings demonstrate gut microbial dysbiosis after burn injury and provide new insights into the burn-related dysbiosis of the gut microbiome and strategies for improving the treatment of burn injury from the perspective of the microbiota.

Diversity of protist genera in periphyton of tufa-depositing karstic river

PurposeIn aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.MethodsProtist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.ResultsThe three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.ConclusionThe combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.

Plasma, urine, and stool metabolites in response to dietary rice bran and navy bean supplementation in adults at high-risk for colorectal cancer.

Dietary intake of whole grains and legumes and adequate physical activity (PA) have been associated with reduced colorectal cancer (CRC) risk. A single-blinded, two-arm, randomized, placebo-controlled pilot trial was implemented to evaluate the impact of a 12-week dietary intervention of rice bran + navy bean supplementation and PA education on metabolite profiles and the gut microbiome among individuals at high risk of CRC. Adults (n=20) were randomized 1:1 to dietary intervention or control. All participants received PA education at baseline. Sixteen study foods were prepared with either heat-stabilized rice bran + navy bean powder or Fibersol®-2 as a placebo. Intervention participants consumed 30 g rice bran + 30 g navy bean powder daily; those in the control group consumed 10 g placebo daily. Non-targeted metabolite profiling was performed by UPLC-MS/MS to evaluate plasma, urine, and stool at 0, 6, and 12 weeks. Stool was also analyzed for primary and secondary bile acids (BAs) and short chain fatty acids (SCFAs) by UPLC-MS/MS and microbial community structure via 16S amplicon sequencing. Two-way ANOVA was used to compare differences between groups for metabolites, and mixed models were used to compare differences between groups for BAs, SCFAs, and alpha and beta diversity measures of microbial community structure. Across biological matrices, the intervention resulted in changes to several amino acid and lipid metabolites, compared to control. There was a 2.33-fold difference in plasma (p<0.001) and a 3.33-fold difference in urine (p=0.008) for the amino acid S-methylcysteine at 12 weeks. Fold-differences to 4-methoxyphenol sulfate in plasma and urine after 6 and 12 weeks (p<0.001) was a novel result from this combined rice bran and navy bean intervention in people. A 2.98-fold difference in plasma (p=0.002) and a 17.74-fold difference in stool (p=0.026) was observed for the lipid octadecenedioylcarnitine at 12 weeks. For stool BAs, 3-oxocholic acid was increased at 12 weeks compared to control within a subset of individuals (mean difference 16.2 ug/uL, p=0.022). No significant differences were observed between groups for stool SCFAs or microbial community structure. Dietary intake of rice bran + navy beans demonstrates beneficial modulation of host and gut microbial metabolism and represents a practical and affordable means of increasing adherence to national guidelines for CRC control and prevention in a high-risk population.

Weanling gut microbiota composition of a mouse model selectively bred for high voluntary wheel-running behavior.

We compared the fecal microbial community composition and diversity of four replicate lines of mice selectively bred for high wheel-running activity over 81 generations (HR lines) and four non-selected control lines. We performed 16S rRNA gene sequencing on fecal samples taken 24 h after weaning, identifying a total of 2074 bacterial operational taxonomic units. HR and control mice did not significantly differ for measures of alpha diversity, but HR mice had a higher relative abundance of the family Clostridiaceae. These results differ from a study of rats, where a line bred for high forced-treadmill endurance and that also ran more on wheels had lower relative abundance of Clostridiaceae, as compared with a line bred for low endurance that ran less on wheels. Within the HR and control groups, replicate lines had unique microbiomes based on unweighted UniFrac beta diversity, indicating random genetic drift and/or multiple adaptive responses to selection.

Determinants of chironomid species richness in mid-European temperate rivers – Environmental factors, regional influences, diversity, and seasons

Multiscale determinants of riverine chironomid species richness were assessed in seven rivers in Central Poland, an area representative of the European temperate climatic zone. The impact of environmental factors, seasonality, as well as the concepts of gamma diversity, i.e. habitat species richness (HSR), alpha diversity, i.e. local species richness (LSR), and the relationships between these, i.e. beta diversity, were studied.One site in each river was defined as a habitat and monthly LSR time series data were obtained at each site over a full annual cycle for analysis. No strong trend in the time series was detected. The autocorrelation function (ACF) indicated that the time series were uncorrelated white noise.A stepwise forward regression model with no HSR indicated that depth, Substrate Index (SI), velocity and dissolved oxygen were significant factors of LSR values in the studied area, explaining together with summer (as a dummy variable) 67.01% of LSR variance (R2adj = 0.66). Seasonality was noticeable in the impact of summer on increase in species richness. When HSR was included in a similar model then it explained, together with benthic particulate organic matter (BPOM), SI, depth, and velocity, 70.90% of variability in LSR variance (R2adj = 0.69), HSR alone accounting for 58.95% in LSR variance (R2adj = 0.59).In both the annual cycle and in given seasons, HSR strongly positively correlated with the minimum, maximum, and mean LSR values, and there was no saturation of the rivers by chironomid species, i.e. other chironomid species were still able to inhabit the rivers beside the present ones. HSR did not correlate with beta diversity when measured by two widely used setwise beta diversity indices, or by three pairwise beta diversity indices. The exception was in autumn, where one setwise and two pairwise beta diversity measures correlated with both alpha and gamma diversity measures, which suggests a greater stability of larval chironomid assemblages in that season. This larval stability was not associated with greater stability of environmental factors in autumn, hence the stability seems to be related to undisclosed biotic mechanisms.Seasonality was also a strong factor in predicting the exchange of species. Turnover index between seasons ranged from 0.133 (spring vs summer) to 0.261 (autumn vs winter) and UPGMA clustering determined least chironomid similarity between winter and other seasons.

Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods.

In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at -80°C for 2 years on the stability of the V4 region of the 16S rRNA gene across seven different collection methods (i.e., no additive, 95% ethanol, RNAlater stabilization solution, fecal occult blood test cards, and fecal immunochemical test tubes for feces; OMNIgene ORAL tubes and Scope mouthwash for saliva) among 51 healthy volunteers. Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha-diversity metrics, and the first principal coordinates of three beta-diversity matrices. The subject variability was much higher than the variability introduced by the sample collection type, and storage time. For fecal samples, microbial stability over 2 years was high across collection methods (range, ICCs = 0.70-0.99), except for the samples collected with no additive (range, ICCs = 0.23-0.83). For oral samples, most microbiome diversity measures were stable over time with ICCs above 0.74; however, ICCs for the samples collected with Scope mouthwash were lower for two alpha-diversity measures, Faith's phylogenetic diversity (0.23) and the observed number of operational taxonomic units (0.23). Fecal and oral samples in most used collection methods are stable for microbiome analyses after 2 years at -80°C, except for fecal samples with no additive. This study provides evidence that samples stored for an extended period from prospective studies are useful for microbiome analyses.

Rectal swabs as a viable alternative to faecal sampling for the analysis of gut microbiota functionality and composition

Faecal or biopsy samples are frequently used to analyse the gut microbiota, but issues remain with the provision and collection of such samples. Rectal swabs are widely-utilised in clinical practice and previous data demonstrate their potential role in microbiota analyses; however, studies to date have been heterogenous, and there are a particular lack of data concerning the utility of swabs for the analysis of the microbiota’s functionality and metabolome. We compared paired stool and rectal swab samples from healthy individuals to investigate whether rectal swabs are a reliable proxy for faecal sampling. There were no significant differences in key alpha and beta diversity measures between swab and faecal samples, and inter-subject variability was preserved. Additionally, no significant differences were demonstrated in abundance of major annotated phyla. Inferred gut functionality using Tax4Fun2 showed excellent correlation between the two sampling techniques (Pearson’s coefficient r = 0.9217, P < 0.0001). Proton nuclear magnetic resonance (1H NMR) spectroscopy enabled the detection of 20 metabolites, with overall excellent correlation identified between rectal swab and faecal samples for levels all metabolites collectively, although more variable degrees of association between swab and stool for levels of individual metabolites. These data support the utility of rectal swabs in both compositional and functional analyses of the gut microbiota.

The gestational membrane microbiome in the presence or absence of intraamniotic infection

Data regarding the microbiome of the gestational membranes are emerging and conflicting. Shifts in the microbial communities in the setting of labor, rupture of membranes, and intraamniotic infection are yet to be understood. This study aimed to characterize the microbiome of the gestational membranes of women in labor or with ruptured membranes, including those with and without intraamniotic infection. Women with a singleton pregnancy at ≥28 weeks' gestation undergoing unscheduled cesarean delivery in the setting of labor or rupture of membranes were included. Demographic and clinical variables were collected. We defined suspected intraamniotic infection by standard clinical criteria; placentae and gestational membranes were also reviewed for histologic evidence of infection. Sterile swabs were collected from membranes at the time of delivery. Bacteria were cultured from the swabs, and the isolates were sequenced. DNA extraction and 16S sequencing of the swabs were also performed. Bacterial taxonomy was assigned to each sequence. Alpha diversity indices and beta-diversity metrics were calculated to test for differences in microbial community diversity and composition between uninfected and infected groups. Differential abundance of bacteria between infected and uninfected groups was tested at the class, family, and genus level. Samples were collected from 34 participants. Clinical intraamniotic infection was diagnosed in 38% of participants, although 50% of placentae and membranes demonstrated histologic signs of infection. Of all samples, 68% grew bacteria on culture; this included 62% of the uninfected samples and 77% of the infected samples (P=.83). Multiple measures of alpha diversity were not significantly different between uninfected and infected groups. Similarly, analysis of beta diversity revealed that the microbial community was not significantly different between the uninfected and infected group. Several bacteria traditionally characterized as pathogenic, including Actinomyces and Streptococcus agalactiae, were identified in both infected and uninfected samples. The pathogenesis and clinical implications of intraamniotic infection remain poorly understood. Diverse bacteria are present in both infected and uninfected gestational membranes. A unique microbiologic signature may exist among the gestational membranes following labor or rupture of membranes, and further characterization of the pathogens specifically implicated in intraamniotic infection may allow for targeted therapy.

Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes.

South Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors. The gut microbiota and gut permeability, as assessed through circulating lipopolysaccharide binding protein (LBP), may underlie the link between chronic inflammation and type 2 diabetes (T2D). The composition of the gut microbiota varies according to multiple factors including demographics, migration, and dietary patterns, particularly fiber intake. However, there is no evidence on the composition of the gut microbiota and its relationship with metabolic health in refugee populations, including those migrating to the United States from Bhutan. The objective of this study was to examine glycemic status in relation to LBP, systemic inflammation fiber intake, and gut microbiota composition in Bhutanese refugee adults residing in New Hampshire (n = 50). This cross-sectional study included a convenience sample of Bhutanese refugee adults (N = 50) in NH. Established bioinformatics pipelines for metagenomic analysis were used to determine relative genus abundance, species richness, and alpha diversity measures from shallow shotgun sequences. The relationships between inflammatory markers, gut microbiota composition, dietary fiber, and glycemic status were analyzed. We identified a substantial chronic disease burden in this study population, and observed a correlation between glycemic status, LBP, and inflammation, and a correlation between glycemic status and gut microbiome alpha diversity. Further, we identified a significant correlation between proinflammatory taxa and inflammatory cytokines. SCFA-producing taxa were found to be inversely correlated with age. To date, this is the most comprehensive examination of metabolic health and the gut microbiome in a Bhutanese refugee population in NH. The findings highlight areas for future investigations of inflammation and glycemic impairment, in addition to informing potential interventions targeting this vulnerable population.