Alpha Diversity Measures Research Articles

Effects of Zinc Source and Enzyme Addition on the Fecal Microbiota of Dogs.

Supplemental zinc from organic sources has been suggested to be more bioavailable than inorganic ones for dog foods. However, the bioavailability of zinc might be affected by dietary constituents such as phytates. The present study aimed to evaluate the effects of two zinc sources (zinc sulfate and zinc proteinate) and the addition of a multi-enzymatic complex from the solid-state fermentation of Aspergillus niger on end-products of fecal fermentation and fecal microbiota of adult Beagles fed a high-phytate diet. The experimental design consisted of three 4 × 4 Latin Squares with a 2 × 2 factorial arrangement of treatments (n = 12 Beagles), with four periods and four diets: zinc sulfate without (IZ) or with (IZ +) enzyme addition, and zinc proteinate without (OZ) or with (OZ +) enzyme addition. Enzyme addition significantly affected Faith’s phylogenetic diversity index, whereas zinc source did not affect either beta or alpha diversity measures. Linear discriminant analysis effect size detected nine taxa as markers for organic zinc, 18 for inorganic source, and none for enzyme addition. However, with the use of a negative binomial generalized linear model, further effects were observed. Organic zinc was associated with a significantly higher abundance of Firmicutes and lower Proteobacteria and Bacteroidetes, although at a genus level, the response varied. The DNA abundance of Clostridium cluster I, Clostridium cluster XIV, Campylobacter spp., Ruminococcaceae, Turicibacter, and Blautia was significantly higher in dogs fed IZ and IZ + diets. Higher abundance of genus Lactobacillus was observed in dogs fed enzyme-supplemented diets. End-products of fecal fermentation were not affected by zinc source or enzymes. An increase in some taxa of the phyla Actinobacteria and Firmicutes was observed in feces of dogs fed organic zinc with enzyme addition but not with inorganic zinc. This study fills a gap in knowledge regarding the effect of zinc source and enzyme addition on the fecal microbiota of dogs. An association of zinc bioavailability and bacteria abundance is suggested, but the implications for the host (dog) are not clear. Further studies are required to unveil the effects of the interaction between zinc sources and enzyme addition on the fecal microbial community.

Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis.

The association of taste genetics and the oral microbiome in autoimmune diseases such as rheumatoid arthritis (RA) has not been reported. We explored a novel oral mucosal innate immune pathway involving the bitter taste G protein-coupled receptor T2R38. This case–control study aimed to evaluate whether T2R38 polymorphisms associate with the buccal microbial composition in RA. Genomic DNA was obtained from buccal swabs of 35 RA patients and 64 non-RA controls. TAS2R38 genotypes were determined by Sanger sequencing. The buccal microbiome was assessed by Illumina MiSeq sequencing of the V4-16S rRNA gene. Bacterial community differences were analyzed with alpha and beta diversity measures. Linear discriminant analysis effect size identified taxa discriminating between RA versus non-RA and across TAS2R38 genotypes. TAS2R38 genotype frequency was similar between RA and non-RA controls (PAV/PAV; PAV/AVI; AVI/AVI: RA 42.9%; 45.7%; 11.4% versus controls 32.8%; 48.4%; 18.8%, chi-square (2, N = 99) = 2.1, p = 0.35). The relative abundance of Porphyromonas, among others, differed between RA and non-RA controls. The relative abundance of several bacterial species also differed across TAS2R38 genotypes. These findings suggest an association between T2R38 polymorphisms and RA buccal microbial composition. However, further research is needed to understand the impact of T2R38 in oral health and RA development.

PSIX-6 Dietary crude protein modifies fecal microbial populations independent of feed efficiency status in dairy cows

Abstract Understanding the composition and structure of the fecal microbial community may provide insight into bacterial adaptation to dietary changes in cattle. The aim of this study was to determine relationships among the fecal microbiome, residual feed intake (RFI) and residual net energy intake (REI) with diets varying in crude protein (CP). Four Holstein lactating cows (806 ± 38 kg of BW) were randomly assigned to one of two treatments (LOW: 13.2% and BASE:16.6% CP) in a crossover design (2 periods of 18 d each). Cows were 260 ± 62 days in milk (DIM) and averaged 26.5 ± 12.0 kg milk yield (MY). Diets were formulated to meet animal needs. Individual feed intake measured by a Calan Gate system was used to calculate daily dry matter intake (DMI). BW, MY and milk components were also measured daily. A linear mixed model with repeated measurements over time was used to evaluate diet effect on DMI, MY, RFI and REI in SAS. Individual fecal samples were collected at the end of each period and extracted DNA was subject to 16S rRNA gene deep amplicon sequencing. Operational Taxonomic Units (OTU) were obtained using ≥97% similarity (SILVA database) and microbial community structure was assessed using alpha and beta diversity measures. No significant differences in phenotypic variables evaluated were observed between treatments or periods. We identified 927 concordant OTU among all cows, with 505 novel OTU identified in BASE cows and 403 in LOW cows. Microbial community structure was similar between treatments and feed efficiency measures. One OTU class, Erysipelotrichi, increased in abundance (P = 0.014) in BASE compared to LOW treatment. Findings reflect previous literature in which Erysipelotrichi was associated with high energy or high fat diets. Although no differences were observed in the phenotypic measurements between treatments, metagenomics analyses indicated differences in specific fecal microbial abundance.

Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

Agriculture causes homogenization of plant‐feeding nematode communities at the regional scale

Abstract An emerging research line in conservation ecology addresses how environmental change drivers may cause the biotic homogenization of ecological communities by shifts in species diversity and community composition. While the drivers have been explored in unmanaged ecosystems and managed agricultural systems, this issue has received limited attention in regard to a key soil bioindicator organisms, soil nematodes. In this study, we evaluated the effect of land‐use change and intensification on the diversity of plant‐feeding nematodes (PFN) though taxonomic and functional measures of alpha and beta diversity. We selected olive tree farms in southern Spain as the study system, given the wide distribution of wild forms in unmanaged systems and cultivated forms in agricultural systems, thus providing the opportunity to assess the effects of land‐use intensity. Notably, our study revealed that the conversion from natural to agricultural systems and even moderate increases in land‐use intensity caused a significant biotic homogenization by enhancing the functional similarities of PFN communities. Our study emphasizes the key role of body size in structuring nematode communities in response to land‐use type and intensity. Synthesis and applications. The importance of soil nematodes in soil processes is well known. We show that land‐use intensification reduces soil nematode diversity. Our study has important implications for the development of management strategies that foster soil biodiversity conservation such as no or minimal tillage and logging, vegetative covers and the maintenance of natural habitat.

Comparison of microbial composition of cough swabs and sputum for pathogen detection in patients with cystic fibrosis

BackgroundWith the continued advancement of CFTR modulator therapies there is likely to be a burgeoning population of adult cystic fibrosis (CF) patients unable to expectorate sputum. Consequently, the detection and surveillance of pulmonary colonisation, previously reliant on sputum culture, needs re-examining. We hypothesised that cough swabs analysed with culture-independent analysis of the 16S gene could serve as a surrogate for colonisation of the lower airways. MethodsCough swabs and sputum samples were prospectively collected from consecutive adults and children with CF across two sites at regular outpatient appointments. Conventional culture analysis and next generation sequencing were used to compare paired same day samples. ResultsTwenty-two adults and 8 paediatric patients provided 75 paired cough swabs and sputum samples. Alpha diversity measures showed increased bacterial richness in sputum, while evenness and Simpson's diveristy index were higher in cough swabs. Within each sampling technique, microbial composition showed greater similarity when considering intra-patient variation. Poor concordance was observed between culture independent cough swabs and culture dependent/independent sputum analysis for specific pathogens, with cough swabs unable to accurately identify commonly associated CF pathogens (AUROCC range: 0.51 to 0.64). ConclusionCulture independent analysis of cough swabs provides an inaccurate diagnosis of lower respiratory tract colonisation and should not be used as a diagnostic test in patients with CF.

Low Diversity in Nasal Microbiome Associated With Staphylococcus aureus Colonization and Bloodstream Infections in Hospitalized Neonates.

Background Staphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Few data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection.MethodsWe performed 2 matched case–control studies (colonization cohort—neonates who did and did not acquire S. aureus colonization; bacteremia cohort—neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in 2 intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge and cultured for S. aureus, and the nasal microbiome was characterized using 16S rRNA gene sequencing.ResultsIn the colonization cohort, 43 S. aureus–colonized neonates were matched to 82 controls. At 1 week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank-sum test P < .05) and differed in beta diversity (omnibus MiRKAT P = .002) even after adjusting for birth weight (P = .01). The bacteremia cohort included 10 neonates, of whom 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared with colonized neonates and controls.ConclusionsThe association of increased S. aureus abundance and decrease of microbiome diversity suggest the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.

Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection.

ABSTRACTIn recent years, our appreciation of the extent of habitable environments in Earth’s subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time.IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota.

Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation.

Minimal Associations between Short-Term Dietary Intake and Salivary Microbiome Composition.

Background: Increasing evidence points to the esophageal microbiome as an important co-factor in esophageal neoplasia. Esophageal microbiome composition is strongly influenced by the oral microbiome. Salivary microbiome assessment has emerged as a potential non-invasive tool to identify patients at risk for esophageal cancer, but key host and environmental factors that may affect the salivary microbiome have not been well-defined. This study aimed to evaluate the impact of short-term dietary intake on salivary microbiome composition. Methods: Saliva samples were collected from 69 subjects prior to upper endoscopy who completed the Automated Self-Administered 24-Hour (ASA24) Dietary Assessment. Salivary microbiome composition was determined using 16S rRNA amplicon sequencing. Results: There was no significant correlation between alpha diversity and primary measures of short-term dietary intake (total daily calories, fat, fiber, fruit/vegetables, red meat intake, and fasting time). There was no evidence of clustering on beta diversity analyses. Very few taxonomic alterations were found for short-term dietary intake; an increased relative abundance of Neisseria oralis and Lautropia sp. was associated with high fruit and vegetable intake, and an increased relative abundance of a taxon in the family Gemellaceae was associated with increased red meat intake. Conclusions: Short-term dietary intake was associated with only minimal salivary microbiome alterations and does not appear to have a major impact on the potential use of the salivary microbiome as a biomarker for esophageal neoplasia.

The association between serum microbial DNA composition and symptoms of depression and anxiety in mood disorders

There is increasing evidence supporting the association between gut microbiome composition and mood disorders; however, studies on the circulating microbiome are scarce. This study aimed to analyze the association of the serum microbial DNA composition with depressive and anxiety symptoms in patients with mood disorders. The sera of 69 patients with mood disorders, aged from 19 to 60, were analyzed. Bacterial DNA was isolated from extracellular membrane vesicles and, subsequently, amplified and quantified with specific primers for the V3–V4 hypervariable region of the 16S rDNA gene. Sequence reads were clustered into Operational Taxonomic Units and classified using the SILVA database. There were no significant associations between alpha diversity measures and the total Hamilton depression rating scale (HAM-D) or Beck anxiety inventory (BAI) scores. Only the weighted UniFrac distance was associated with the total HAM-D score (F = 1.57, p = 0.045). The Bacteroidaceae family and Bacteroides genus were negatively associated with the total HAM-D score (β = − 0.016, p < 0.001, q = 0.08 and β = − 0.016, p < 0.001, q = 0.15, respectively). The Desulfovibrionaceae family and Clostridiales Family XIII were positively associated with the total BAI score (β = 1.8 × 10−3, p < 0.001, q = 0.04 and β = 1.3 × 10−3, p < 0.001, q = 0.24, respectively). Further studies with larger sample sizes and longitudinal designs are warranted.

Spatiotemporal pattern of shark biodiversity in the Eastern and Central Pacific Ocean

Sharks are one of the most threatened groups of marine animals, as high exploitation rates combined with low resilience to fishing pressure have led to population declines worldwidely. Designing conservation strategies for sharks depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. In this study, observer data from 1 874 sets of Chinese tuna longline fisheries in the Eastern and Central Pacific were used to estimate the biodiversity of sharks by applying alpha diversity measures, such as species richness, Chao2 index, Shannon index, species evenness, species density and rank-abundance curves, and the relationships of species richness and Shannon index with spatiotemporal and environmental factors, such as year, season, latitude, longitude, sea surface temperature, chlorophyll-a, and sea level anomaly were analyzed using the generalized additive models. Results showed that a total number of 20 sharks were observed, mainly consisting of <italic>Prionace glauca</italic> and <italic>Carcharhinus falciformis</italic> in the Eastern and Central Pacific. We found that there was a similar species composition in the Eastern and Central Tropical Pacific (Chao2=23.98) and Southeastern Pacific (Chao2=22.50), but the species evenness in the Tropical Pacific was higher than that in the Southeastern Pacific. The shark community in the Eastern and Central Tropical Pacific was dominated by <italic>Prionace glauca</italic> (28.97%) and <italic>Carcharhinus falciformis</italic> (23.85%), while in the Southeastern Pacific it was overwhelmingly dominated by <italic>Prionace glauca</italic> (76.64%). In the Eastern and Central Pacific, the biodiversity of sharks, such as species richness (<italic>S</italic>), Shannon Index (<italic>H</italic>’), and species density in the tropical area was higher than that in the temperate area. The species richness and diversity of sharks showed large spatiotemporal differences and were significantly influenced by habitat environmental characteristics. In terms of inter-annual variation, shark community diversity showed an increasing trend from 2012 to 2017 and a slight decrease from 2017 to 2019. The season with the highest diversity was the third season and the lowest diversity was found in the first season. Sharks preferred to inhabit the areas characterized by warm waters (sea surface temperature≈25℃), intermediate productivity concentrations (chlorophyll-a>0.10 mg·m^-3) and abnormally low sea level (sea level anomaly < 0 m). The alpha diversity performed well in identifying hotspots of biodiversity. The study helps to understand the shark biodiversity in pelagic ecosystems and identify, for conservation purposes, the critical habitats of the shark’s community in tuna longline fisheries in the Eastern and Central Pacific Ocean, and contributes to the future implementation of the protected marine areas, fishing moratorium or restricted fishing zone to manage the pelagic ecosystem in a holistic and more integrated way.

Grab what you can-an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding.

Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.

Markers of metabolic health and gut microbiome diversity: findings from two population-based cohort studies

Aims/hypothesisThe gut microbiome is hypothesised to be related to insulin resistance and other metabolic variables. However, data from population-based studies are limited. We investigated associations between serologic measures of metabolic health and the gut microbiome in the Northern Finland Birth Cohort 1966 (NFBC1966) and the TwinsUK cohort.MethodsAmong 506 individuals from the NFBC1966 with available faecal microbiome (16S rRNA gene sequence) data, we estimated associations between gut microbiome diversity metrics and serologic levels of HOMA for insulin resistance (HOMA-IR), HbA1c and C-reactive protein (CRP) using multivariable linear regression models adjusted for sex, smoking status and BMI. Associations between gut microbiome diversity measures and HOMA-IR and CRP were replicated in 1140 adult participants from TwinsUK, with available faecal microbiome (16S rRNA gene sequence) data. For both cohorts, we used general linear models with a quasi-Poisson distribution and Microbiome Regression-based Kernel Association Test (MiRKAT) to estimate associations of metabolic variables with alpha- and beta diversity metrics, respectively, and generalised additive models for location scale and shape (GAMLSS) fitted with the zero-inflated beta distribution to identify taxa associated with the metabolic markers.ResultsIn NFBC1966, alpha diversity was lower in individuals with higher HOMA-IR with a mean of 74.4 (95% CI 70.7, 78.3) amplicon sequence variants (ASVs) for the first quartile of HOMA-IR and 66.6 (95% CI 62.9, 70.4) for the fourth quartile of HOMA-IR. Alpha diversity was also lower with higher HbA1c (number of ASVs and Shannon’s diversity, p < 0.001 and p = 0.003, respectively) and higher CRP (number of ASVs, p = 0.025), even after adjustment for BMI and other potential confounders. In TwinsUK, alpha diversity measures were also lower among participants with higher measures of HOMA-IR and CRP. When considering beta diversity measures, we found that microbial community profiles were associated with HOMA-IR in NFBC1966 and TwinsUK, using multivariate MiRKAT models, with binomial deviance dissimilarity p values of <0.001. In GAMLSS models, the relative abundances of individual genera Prevotella and Blautia were associated with HOMA-IR in both cohorts.Conclusions/interpretationOverall, higher levels of HOMA-IR, CRP and HbA1c were associated with lower microbiome diversity in both the NFBC1966 and TwinsUK cohorts, even after adjustment for BMI and other variables. These results from two distinct population-based cohorts provide evidence for an association between metabolic variables and gut microbial diversity. Further experimental and mechanistic insights are now needed to provide understanding of the potential causal mechanisms that may link the gut microbiota with metabolic health.Graphical abstract

Extensive sex-specific and regional variations observed in the microbiome of Dermacentor reticulatus

Recent progress in DNA sequencing technologies and advanced bioinformatic tools have enabled researchers to rapidly decipher the tick microbiome. To date, however, a number of microbiome studies performed on Dermacentor reticulatus ticks is still quite limited. Despite the importance of this ixodid tick for veterinary and human medicine, only two investigations have examined its microbiome. Moreover, these studies analyzed only a limited number of ticks/tick pools. Given the scarcity of microbiome data for D. reticulatus in general and the lack of microbiome studies on tick species from Eastern Europe in particular, the objective of the current investigation was to analyze the microbiome of D. reticulatus ticks collected from three geographical regions of Ukraine. A total of 88 individual tick microbiomes were analyzed by sequencing the V6 region of 16S rRNA. As a result, numerous significant differences in the bacterial relative abundance were detected between males and females of D. reticulatus for each region. The alpha diversity measures indicate that microbiomes were significantly different between females of D. reticulatus inter-regionally. In contrast, the collective results for male ticks are more suggestive of inter-regional microbiome homogeneity. The overall findings indicate that the composition and diversity of the D. reticulatus microbiome can be impacted by geographical and sex-related factors.

Environmental Influences on the Human Gut Microbiota: A Longitudinal Pilot Study

ObjectivesUrbanization has reduced environmental microorganism exposure, with most Americans spending over 90% of their time indoors. However, gardening remains a viable means of exposure to soil microorganisms and harvesting of edible produce. Accordingly, we aimed to determine relations between gardening, dietary habits, and gut microbiota. MethodsGardening families (N = 10) and non-gardening (control) families (N = 9) were enrolled in a longitudinal pilot trial. Families included two adults and a child (5–18 years) for a total sample size of 54 participants. Fecal samples were collected prior to and at the end of the gardening season. Garden soil samples (n = 9) were collected prior to and at the end of the season. Diet history questionnaires were collected at the beginning and end of the study to measure Healthy Eating Index (HEI) scores. Fecal and soil DNA were extracted, sequenced (V4 region of 16S rDNA gene), and analyzed using DADA2 and QIIME2. Alpha diversity measures were assessed, including Faith’s phylogenetic diversity (PD) and observed operational taxonomic units (OTUs). ResultsGardening families had significantly more fecal OTUs compared to control families (172.3 ± 44.2 vs. 157.0 ± 44.2, respectively; P = 0.03). Gardening families had greater (P = 0.02) Faith’s PD scores and tended (P = 0.08) to have more fecal OTUs than the control group at peak gardening season. In the gardening families, fecal OTUs and Faith’s PD were numerically but not statistically greater at the end of the season compared to baseline (all p’s > 0.05). Prior to the gardening season, gardening adults had greater HEI scores compared to control families (57 ± 9.1 vs. 49 ± 8.8, P = 0.03). HEI scores were not different between groups at the end of the study. ConclusionsThis study revealed that the fecal microbiota of families that garden differs from non-gardening families, and there are detectable changes in the fecal microbial community of gardeners and their family members over the course of the gardening season. Further research is needed to understand the role of diet in these changes and if microbes within the soil move between the soil and gastrointestinal environments. Funding SourcesThis research was funded by the Christopher Family Foundation Food and Family Grant Program.

Black Raspberry Supplementation Alters the Gut Microbiome and Improves Alpha Diversity in a Mouse Model of Inflammation-Associated Colorectal Cancer

ObjectivesAnti-inflammatory bioactives in black raspberries (BRB) have been shown to have protective effects on the colon epithelium and may influence gut microbiome. The goal of this study was to determine the effects of dietary intervention with BRB on the dynamic composition of the gut microbiome composition in mice. MethodsUsing a 2 × 2 factorial design, C57BL/6J male mice were fed the standard AIN93G diet or the total Western diet (TWD) for 16 weeks with or without 10% (w/w) whole, freeze-dried BRB powder. The azoxymethane + dextran sodium sulfate model of inflammation-associated colorectal cancer was employed to assess the dynamic response of the gut microbiome to basal diet and BRB treatment prior to, during, and after active colitis and at the study end. Microbiome composition was determined using 16s rRNA sequencing followed by diversity analyses (alpha and beta) and identification of discriminating taxa by with linear discriminant analyses by effect size (lefse). ResultsAlpha diversity was markedly reduced during colitis for mice consuming either AIN93G or TWD, with some improvement noted by the recovery phase. Of note, consumption of BRB for two weeks significantly increased alpha diversity measures, and BRB improved alpha diversity in mice fed the AIN93G diet during colitis. Alternatively, BRB appeared less effective in mice fed TWD. Beta diversity was also significantly affected with notable clustering of microbiomes by BRB treatment during and after colitis. Consumption of BRB affected the relative abundance of several key taxa over the course of colitis and recovery from gut injury, including Erysipelotrichaceae, Bifidobacteriaceae, Streptococcaceae, Rikenellaceae, Ruminococcaceae and Akkermansiaceae, among others. ConclusionsDietary supplementation with BRB shifted the composition of the gut microbiome during colitis and recovery from gut injury, though the effects were inconsistent with respect to the basal diet consumed. Funding SourcesUSDA NIFA AFRI grant no. 2018-67017-27,516 and 2014-67017-21755.

Gut microbiome diversity and composition is associated with hypertension in women.

Objectives:Animal studies support a role for the gut microbiota in hypertension development, but large human studies are lacking. Here, we investigated the relationship between hypertension prevalence and gut microbial composition in two cohorts.Methods:We included 871 unrelated TwinsUK women with faecal microbiome data (16s rRNA gene sequencing). Multivariable linear models adjusted for age, age2 and BMI as well as MiRKAT models, were used to estimate the association of hypertension with alpha- and beta-diversity metrics. To identify taxa associated with hypertension, a generalized additive model for location scale and shape was computed adjusting for covariates and multiple testing. Results were replicated in 448 women from PREDICT-1.Results:We found that measures of alpha diversity are significantly lower in hypertensive cases [Beta(95% confidence interval, 95% CI) = −0.05 (−0.095 to −0.004), P = 0.03] and a significant association between beta diversity and hypertension (FDR < 0.05). We identified and replicated two genera associated with hypertension. The genus, Ruminiclostridium 6 was less abundant in hypertension cases [meta-analysis (95% CI) = −0.31 (−0.5 to −0.13), P = 1 × 10−3]. The uncultured microbe Erysipelotrichacea-UCG003 was more abundant in hypertensive cases [meta-analysis (95% CI) = 0.46 (0.3–0.62), P = 1 × 10−4]. We genomically analysed the 16 s rRNA sequence and established a 100% identity match with the 16 s rRNA sequence of the genus Faecalibacillus. We functionally annotated Ruminiclostridium, identifying 83 metabolic pathways, including pathways previously linked to blood pressure regulation.Conclusion:In this large human observation, we show that gut microbiome diversity and composition are associated with hypertension. Our results suggest that targeting the microbiome may be a novel means to prevent or treat hypertension.

114 Stability of Gut Microbiome Alpha Diversity During Combined Sleep Restriction and Circadian Misalignment

Abstract Introduction Disturbed gut microbiome diversity has been associated with poor health outcomes and various disease states. We investigated the impact of combined sleep restriction (3h time in bed [TIB] sleep opportunities per day) and circadian misalignment (daytime sleep and nighttime wakefulness) on gut microbiome alpha diversity in healthy young individuals in a controlled laboratory setting. Methods Twenty healthy adults (8 female), mean age (±SD) 25.65(±4.2) completed a 39-day protocol consisting of two laboratory visits lasting 4 days each. Two weeks of ambulatory monitoring prior to laboratory visits confirmed ~8h habitual sleep duration per night. Participants consumed energy-balanced diets, identical within participants, 2 days before and during the laboratory visits. The laboratory visits consisted of sleep opportunities as follows: night 1 (8h TIB), night 2 (3h TIB), day 3 (3h TIB) and day 4 (3h TIB). Fecal microbiome samples were obtained at baseline between day 1 and 2, and during sleep and circadian disruption (between day 3 and 4). Alpha diversity measures were calculated using Pielou’s evenness, Faith’s phylogenetic diversity and number of observed OTUs. Results Linear mixed models with subject as a random factor and visit as a fixed factor were performed to assess whether any alpha diversity measures changed during sleep and circadian disruption compared to baseline. Alpha diversity did not change significantly between baseline and sleep and circadian disruption (all p &amp;gt; 0.57). Additionally, intraclass correlation coefficients (ICCs) were calculated at baseline and during sleep and circadian disruption to determine if alpha diversity measures showed trait-like stability at both time points. ICCs were substantial to almost perfect (ICC 0.64–0.84) at baseline and substantial (ICC 0.70–0.80) during sleep and circadian disruption. Conclusion Four days of combined sleep restriction and circadian misalignment does not appear to alter alpha diversity of gut microbiota species in healthy adults. Further, substantial to almost perfect intraclass correlation coefficients suggest alpha diversity of the human microbiome is stable during combined sleep and circadian perturbation and that examination at the level of microbiota community composition and functional outcomes are needed. Support (if any) Office of Naval Research MURI (N00014- 15-1-2809), NIH/NCATS (UL1TR002535), NIH T32 HL149646, CU Undergraduate Research Opportunities.

Latitudinal variation in the diversity–disturbance relationship demonstrates the context dependence of disturbance impacts

AbstractAimThe shape of the diversity–disturbance relationship is context dependent, but the mechanisms driving this context dependence are unclear due to limited standardized empirical assessments across different environmental and ecological settings. At seven sites and over 20° of latitude, spanning both temperate and tropical systems, we measured community response to a fine‐scale experimental disturbance gradient in communities of benthic invertebrates.LocationEast coast of Australia (16.48–36.43° S).Time periodSixty‐six weeks (August 2012–November 2013).Major taxa studiedBenthic marine invertebrates.MethodsCommunities were grown on acrylic tiles and subjected to four experimental disturbance events over a 66‐week period. At the end of this period, the effect of increasing disturbance extent (from 0% to 100% community clearance) on measures of alpha and beta diversity were assessed.ResultsIn the tropics, richness and diversity increased with disturbance because the creation of free space allowed for the colonization of new recruits. In temperate communities, increasing disturbance led to a monotonic loss in species richness and a more hump‐shaped relationship in evenness and diversity. In the tropics, compositional change with increasing disturbance was driven by changes in species identities and abundances as the cover of rare species increased. In temperate regions, however, differences in species abundances were primarily responsible for compositional changes, reflecting the shift to algal dominance in conditions of high disturbance.Main conclusionsThe shape of the diversity–disturbance relationship changed over latitude, indicating that the concept of “intermediate” disturbance differs amongst these communities. Faster rates of increases in bare space, loss of species richness and a shift to algal dominance suggest that, in these systems, higher‐latitude communities are more susceptible to negative outcomes of high levels of disturbance than lower‐latitude communities. We discuss how differences in community dynamics, including competition, regional diversity and availability of propagules, help to explain this pattern.