Faith's Phylogenetic Diversity Research Articles

Infection with Ascaridia galli Does Not Significantly Alter Intestinal Microbiota and Is Cleared After Changes in the Expression of Cytokines.

Because of the trend of cage-free egg production, infections with the nematode Ascaridia galli are receiving increased attention. The aim of this study was to establish a timeline for the influence of A. galli on the expression of key cytokines related to a parasitic immune response, and on the composition of the jejunal microbiota. Twenty-eight male layer-type birds were challenged at 24, 25, and 26 days of age. An additional 28 birds were kept as uninfected controls. Starting on Day 31, three birds of each group were euthanized every week until 8 wk postinfection (PI). The number of larvae isolated from the intestinal wall decreased over time, until no larvae were seen at 7 and 8 wk PI. At 5 wk PI, there was a numerical upregulation of all cytokines (TGF-β, IFN-γ, IL-4, IL-8, IL-10, IL-13) in the infected group, but this change was only statistically significant for IL-13. At this time point, larvae were expected to have developed into adults that would have shed eggs in the feces. However, no adult worms were seen and there was no egg shedding. For the microbiota analysis, there were significant differences in the alpha diversity (Faith's phylogenetic diversity) between challenge and control groups, and the beta diversity analysis showed slight differences between samples, suggesting that the age of the birds was the main reason for the separation of groups. These findings suggest that the upregulation of all cytokines evaluated in Week 5 might be the reason for resolution of the infection. Possible explanations are that a high infection dose and the fact that birds were fed with a more nutritionally dense feed might have contributed to the birds' immune system clearing the infection before the worms were able to reach maturity.

The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study.

The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faith's Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r=-.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls.

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts

Previous studies suggest an interaction of CD36 genetic variant rs1527483 with n-3 polyunsaturated fatty acids (PUFAs) to modulate blood lipids. However, successful replication is lacking and the role of gut microbiome remains unclear. Here, we aimed to replicate these gene-diet interactions on blood lipids and investigate their possible associations with gut microbiome. We evaluated the n-3 PUFA-rs1527483 interaction on blood lipids in two population-based cohorts (n=4,786). We profiled fecal microbiome and short-chain fatty acids among 1,368 participants. The associations between n-3 PUFAs and bacterial alpha-diversity, taxonomies and short-chain fatty acids by rs1527483 genotypes were analyzed using regression models. CD36 rs1527483-GG carriers responded better to high n-3 PUFA exposure; higher blood HDL-C (beta (95% CI): 0.05 (0.01, 0.08) mmol/L) and lower TG (log-transformed, beta (95% CI):-0.08 (-0.14,-0.02)) were observed among participants whose n-3 PUFA exposure ranked in the top quartile comparing with those in the bottom quartile. We identified docosahexaenoic acid (DHA) as the driven individual n-3 PUFA biomarker, which showed interaction with rs1527483. Among the rs1527483-GG carriers, but not other genotype groups, DHA exposure was positively associated with bacterial Faith's phylogenetic diversity, Observed OTUs, Shannon's diversity index, Dorea, Coriobacteriales Incertae Sedis spp, and fecal propionic acid levels. Another independent longitudinal cohort validated the DHA-rs1527483 interaction on gut microbiome. The identified microbial features were correlated with blood lipids, and the host biosynthesis and metabolism pathways of bile acids and aromatic amino acids. The present study found that higher n-3 PUFAs were associated with improved blood lipids and gut microbial features only among rs1527483-GG carriers. These findings highlight a potential role of gut microbiome to link the CD36 genetic variant, n-3 PUFAs and blood lipids, revealing a new research direction to interpret the gene-diet interaction for cardiometabolic health.

Longitudinal urinary microbiome characteristics in women with urgency urinary incontinence undergoing sacral neuromodulation.

The objective was to evaluate the stability of the urinary microbiome communities in women undergoing sacral neuromodulation (SNM) for urgency urinary incontinence (UUI). We hypothesized that clinical response to SNM therapy would be associated with changes in the urinary microbiome. Women completed the Overactive Bladder Questionnaire Short-Form, the International Consultation on Incontinence Questionnaire Short Form, and the Female Sexual Function Index at baseline and 3 months post-SNM implantation. Transurethral urinary specimens were obtained for microbiome analysis at baseline and 3 months postoperatively. The V4 region of the 16S rRNA gene (515F-806R) was amplified with region-specific primers, and Amplicon Sequence Variants (ASVs) were identified with a closed-reference approach of taxonomic classification. Alpha-diversity was calculated using the phylogenetic (i.e., Faith's phylogenetic diversity) and nonphylogenetic metrics (i.e., Shannon diversity, and Pielou's evenness) using the QIIME2 plugin. Longitudinal paired volatility analysis was performed using the DEICODE and Gemelli plugin to account for host specificity across both time and space. Nineteen women who underwent SNM and provided both baseline and 3-month urine samples were included in this analysis. Women reported improvement in objective (number of UUI episodes) and subjective (symptom severity and health-related quality of life) measures. Ninety percent of the bacteria were classified as Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. No significant differences were observed in each subject's beta-diversity at 3 months compared with their baseline microbiome. Our descriptive pilot study of a cohort of women who had achieved objective and subjective improvements in UUI following SNM therapy demonstrates that the urinary microbiome remains relatively stable, despite variability amongst the cohort.

Effects of urbanization on woody plant phylogenetic diversity and its associations with landscape features in the high latitude northern hemisphere region, Northeast China

Urbanization is one of the primary drivers of terrestrial modification, with marked biological homogenization worldwide but relatively poor knowledge of woody phylogenetic diversity. Here, we investigated 943 plots, about 93,000 woody plants from 130 species in Northeast China, and calculated six phylogenetic diversity indexes, and urbanization landscape metrics; the responses of phylogenetic diversity to urbanization and its coupling relationship with landscape features were explored at 25 km × 25 km, 50 km × 50 km and 75 km × 75 km grid scales. We found that urbanization had enhanced the evolutionary distinctiveness of woody plants, characterizing as increasing Faith phylogenetic diversity (FPD) and their mean pairwise distance (MPD) while decreasing the mean nearest taxon distance (MNTD); these trends were independent of landscape scales and gymnosperm inclusion or not. As indicated by increasing SesMPD (Standardized MPD), the dominant role of community assemblage changed from environmental filtering in low urbanization intensity (UI) to competitive exclusion in high UI regions. Artificial surface area (ASA) and its percentage, SHAPE_F (Shape index of forest), and PD_F (Patch density of forest) had a threshold effect on phylogenetic diversity. ASA%, GDP (gross domestic product), and population density were the most potent predictors for the variations of phylogenetic diversity, and GDP contributed the most (42.9%). A higher GDP accompanied a higher FPD, SesPD (Standardized FPD), and SesMNTD (Standardized MNTD); higher PD_F and lower SHAPE_F were associated with higher MNTD, MPD, and SesMPD. In conclusion, urbanization strongly modifies woody plant phylogenetic diversity. Identifying the threshold effects and significant factors for phylogenetic variations allows biodiversity assessment and conservation through proper landscape configuration under the urbanization context.

Dung beetles maintain phylogenetic divergence but functional convergence across a highly fragmented tropical landscape

Abstract Understanding how human‐modified landscapes affect the phylogenetic composition and assembly mechanisms of biological communities is critical for effectively managing and restoring tropical ecosystems. We evaluated how forest coverage loss, fragmentation and landscape heterogeneity affect the phylogenetic diversity of dung beetles and their assembly mechanisms in Los Tuxtlas Biosphere Reserve, a protected but highly fragmented tropical landscape. We calculated Faith's phylogenetic diversity, mean pairwise phylogenetic distance and mean nearest taxon distance for 5,388 individuals in 36 species. The standardised effect sizes of these metrics were estimated to control their correlation with species richness. Phylogenetic diversity was also assessed separately for each dung beetle functional group. Finally, we compared the mean functional and phylogenetic pairwise distance and mean nearest taxon distance and measured the phylogenetic signal among dung beetle functional traits to determine the influence of niche conservatism on the phylogenetic structure of species assemblages. Faith's phylogenetic diversity of dung beetles was positively correlated with forest coverage, while their mean phylogenetic and nearest taxon distance values decreased with increasing landscape fragmentation. Necrophagous beetles and forest specialists responded most negatively to forest coverage loss and fragmentation. Alpha and beta diversity values showed phylogenetic overdispersion but functional convergence and weak phylogenetic signals in their functional traits, suggesting low niche conservatism. Landscapes with moderate forest coverage (≥40%) favoured higher phylogenetic beta diversity, whereas phylogenetic and functional beta diversity decreased significantly in landscapes with low forest coverage (<30%). Synthesis and applications. Forest habitats in fragmented landscapes are essential for safeguarding the evolutionary history of dung beetles, reducing biotic homogenisation processes by favouring phylogenetic overdispersion and complementarity between sites. Therefore, to secure the phylogenetic diversity of dung beetles within fragmented tropical reserves, we recommend protecting the existing forests, preventing further fragmentation of continuous forest areas and increasing matrix quality by implementing biodiversity‐friendly production systems. Finally, managers should consider assessing different functional groups in other species, as their response to landscape disturbance may not be phylogenetically similar. The above will allow more effective management practices to protect the species most susceptible to disturbances.

Changes in Oral Microbial Diversity in a Piglet Model of Traumatic Brain Injury

The dynamic changes in the oral microbiome in response to disease has led to significant interest in utilizing microbiome analysis as a potential diagnostic and prognostic biomarker. Oral dysbiosis has been linked to the progression of neurological diseases such as Alzheimer’s and Parkinson’s diseases, however, no studies have been conducted to evaluate microbiome changes in traumatic brain injury (TBI). This study aimed to examine the changes in the oral microbiome structure during the acute stage of TBI in a clinically translational pig model.Landrace piglets (4‐5 weeks old, male) underwent either a controlled cortical impact surgery (TBI, n=6) or sham surgery (Sham, n=6). TBI was confirmed by magnetic resonance imaging 1 day post‐TBI. Oral swabs of the inside of upper and lower lips, both cheeks, and under the tongue were collected to sample the oral mucosa pre‐surgery and 1, 3, and 7 days post‐surgery (PS). Bacterial DNA was extracted and the V3‐V4 region of 16s rRNA gene was amplified and sequenced using an Illumina NovaSeq platform. Alpha‐, beta‐diversity, and oral microbial composition at the phylum (P), family (F), genus (G), and species (S) level were examined using Qiime2 plugins. Mixed effects ANOVA was used to compare differences between the groups and time points.Significant time effects were identified in several alpha‐diversity indexes during the acute stage of TBI: The number of observed features, Faith’s Phylogenetic Diversity, Shannon Index, and Pielou’s Evenness. However, no group effects were found between TBI and Sham groups, except for Faith’s Phylogenetic Diversity. Faith’s Phylogenetic Diversity showed group and time‐by‐group effects including a significant difference between groups at 7 days PS. In both TBI and Sham groups, beta‐diversity was significantly different between time points and distinct microbial patterns were observed between TBI and Sham groups at 1, 3, and 7 days PS, with the most apparent difference at 7 days PS. Changes in oral microbial composition did not differ between TBI and Sham groups at any taxonomic level (P, F, G, and S), while significant time effects were found in several microbial taxa. Interestingly, significant time‐by‐group effects were found in P_Proteobacteria, F_Leptotrichiaceae, F_Micrococcaceae, and G_Rothia.In conclusion, species diversity as measured by Faith’s Phylogenetic Diversity was lowest at 7 days PS in TBI group compared to Sham group, and TBI and Sham groups showed significant differences in beta‐diversity. With respect to individual microbial taxa, the oral microbial composition was not significantly different between the two groups during the acute stage of TBI. Future studies are needed to investigate further changes in oral microbiome during the chronic stages of TBI.

How different is the forest on post-coal mine heap regarded as novel ecosystem?

Forests are the dominant terrestrial ecosystems on the Earth. During natural succession, a quite known pattern of changes occur (i.e., the process of a gradual assemblage of plant species and associated organisms best adapted to the current habitat conditions). Much less is known about novel ecosystem establishment's primary spontaneous successional mechanisms due to human agency such as post-coal mine heaps habitats. The post-coal mine heaps are sites of pure mineral substrates and constrain (e.g., temperature, acidity, drought, salinity) habitat conditions. These conditions are variable both in time and space. Regardless of all these constraints, diverse vegetation is soon spontaneously developing on these sites. A characteristic feature of the vegetation successional development on post-coal mine heaps is the emergence of non-analogous species assemblages when comparing to the natural and seminatural vegetation communities and ecosystems.This study aimed to compare the forest spontaneously developed on the mineral novel material habitat of the post-coal mining heap, with forests in the surrounding, on non-industrial habitats (located in Silesian Upland (South Poland)) in taxonomic, phylogenetic, and functional diversity at alpha (within-site) and beta (among sites) levels. The functional traits values of the recorded species composition were calculated to assess, e.g., the taxonomic alpha diversity Shannon's diversity and evenness index, Simpson index, functional richness (FRic), functional dispersion (FDis), functional divergence (FDA), and functional evenness (FEve). Rao's entropy has standardized the Biotic Novelty Index (BNI) to reflect the proportion of functional diversity contributed by novel species composition.The results revealed higher functional richness and dispersion in coniferous forests than in forests on heaps. The plots from coniferous forests and heaps were distinctly differentiated in terms of species composition. No difference occurred in functional evenness and divergence. Vegetation patches of coniferous forests had 19% higher species richness and twice higher Faith's phylogenetic diversity, while no differences in species diversity described by Shannon's diversity index have been recorded. An almost thirty times higher biological novelty index in forests on heaps than in coniferous forests patches has been recorded. The RLQ - analysis of relationships between plant traits, species composition and environmental variables revealed significant associations between EIVs and type of habitat and plant traits. The plant traits such as SLA and SM seem indifferent and do not differentiate the two studied habitats.The results showed that both understanding mechanisms by which these habitats are shaped and recognizing their biological potential and values are essential for nature conservation and management and challenge future studies.

Effects of a Low-Carbohydrate, High-Protein Diet on Gut Microbiome Composition in Insulin-Resistant Individuals With Chronic Spinal Cord Injury: Preliminary Results From a Randomized Controlled Trial

ObjectiveTo evaluate the effect of a low-carbohydrate, high-protein (LC/HP) diet that includes healthy dietary components (eg, lean meat, whole grains, fruits and vegetables, fiber, etc) on the gut microbiome composition in individuals with chronic spinal cord injury (SCI). DesignA single-center randomized parallel controlled trial. SettingResearch University. ParticipantsAdult participants with chronic SCI (N=19, 3 years or more after the injury, C2-L2, American Spinal Injury Association Impairment Scale A-D). Participants were insulin resistant and had not received antibiotics within 4 weeks before enrolling in the study. InterventionsParticipants were randomized to the LC/HP diet group (40% energy from carbohydrates, 30% energy from protein, and 30% energy from fat and met dietary guideline recommendations) or the control group for 8 weeks. Participants assigned to the LC/HP group were provided with all meals delivered weekly to their homes. Participants assigned to the control group were asked to continue their usual diet. Main Outcome MeasuresStool samples were collected at baseline and the end of week 8. The gut microbiome 16S ribosomal RNA V4 region was sequenced, and gut microbiome diversity and taxonomical abundance were computed using the QIIME2 suite. ResultsParticipants in the LC/HP group had significant changes in alpha-diversity (reduced operational taxonomic unit and Faith's phylogenetic diversity) and beta-diversity (unweighted UniFrac), while no significant differences were observed among participants in the control group after the intervention. Moreover, several taxa changed differently over time between groups, including increased Bacteroides thetaiotaomicron, Coprococcus 3, Fusicatenibacter, Tannerellaceae, and decreased Tyzzerella, Phascolarctobacterium, Romboutsia, Clostridium sensu stricto 1, Hungatella, Ruminococcus gauvreauii, family XI, and Bacillales among participants in the diet group, while these taxa did not change in the control group. ConclusionsAn LC/HP diet with healthy dietary components improved gut microbiome composition in individuals with SCI, including increased bacteria implicated in fiber metabolism and reduced bacteria communities linked to cardiometabolic disorders.

Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles.

In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.

A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic.

The COVID-19 pandemic poses a great challenge to global public health. The extraordinary daily use of household disinfectants and cleaning products, social distancing and the loss of everyday situations that allow contact between individuals, have a direct impact on the transfer of microorganisms within the population. Together, these changes, in addition to those that occur in eating habits, can affect the composition and diversity of the gut microbiota. A two-time point analysis of the fecal microbiota of 23 Metropolitan Buenos Aires (BA) inhabitants was carried out, to compare pre-pandemic data and its variation during preventive and compulsory social isolation (PCSI) in 2020. To this end, 23 healthy subjects, who were previously studied by our group in 2016, were recruited for a second time during the COVID-19 pandemic, and stool samples were collected from each subject at each time point (n = 46). The hypervariable region V3-V4 of the 16S rRNA gene was high-throughput sequenced. We found significant differences in the estimated number of observed features (p < 0.001), Shannon entropy index (p = 0.026) and in Faith phylogenetic diversity (p < 0.001) between pre-pandemic group (PPG) vs. pandemic group (PG), being significantly lower in the PG. Although no strong change was observed in the core microbiota between the groups in this study, a significant decrease was observed during PCSI in the phylum Verrucomicrobia, which contributes to intestinal health and glucose homeostasis. Microbial community structure (beta diversity) was also compared between PPG and PG. The differences observed in the microbiota structure by unweighted UniFrac PCoA could be explained by six differential abundant genera that were absent during PCSI. Furthermore, putative functional genes prediction using PICRUSt infers a smaller predicted prevalence of genes in the intestinal tryptophan, glycine-betaine, taurine, benzoate degradation, as well as in the synthesis of vitamin B12 during PCSI. This data supports the hypothesis that the microbiome of the inhabitants of BA changed in the context of isolation during PCSI. Therefore, these results could increase the knowledge necessary to propose strategic nutraceutical, functional food, probiotics or similar interventions that contribute to improving public health in the post-pandemic era.

The Gut Microbiome, Seleno-Compounds, and Acute Myocardial Infarction.

Background: Gut microbiome alterations might be considered a metabolic disorder. However, the relationship between the microbiome and acute myocardial infarction (AMI) has not been properly validated. Methods: The feces of 44 subjects (AMI: 19; control: 25) were collected for fecal genomic DNA extraction. The variable region V3–V4 of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The metabolite amounts were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Results: The bacteria were more enriched in the AMI group both in the observed operational taxonomic units (OTUs) and faith phylogenetic diversity (PD) (p-value = 0.01 and <0.001 with 95% CI, individually). The Selenomonadales were less enriched in the AMI group at the family, genus, and species levels (all linear discriminant analysis (LDA) scores > 2). Seleno-compounds were more abundant in the AMI group at the family, genus, and species levels (all LDA scores > 2). Conclusions: This is the first study to demonstrate the association of Selenomonadales and seleno-compounds with the occurrence of AMI. Our findings provide an opportunity to identify a novel approach to prevent and treat AMI.

Intercolony Comparisons of Gut Microbiome Composition From Lab Reared Eastern Subterranean Termites (Blattodea: Rhinotermitidae).

Termites are social insects living in colonies composed of worker, soldier, and reproductive castes. Termite hindguts are inhabited by all three domains of life- Eukarya (protists), Bacteria, and Archaea. These gut microorganisms are horizontally and vertically transferred by nestmates and reproductives, respectively. Prior evidence suggests that every colony potentially has a different gut microbiome that was transferred vertically and horizontally over time. However, we do not know if different colonies reared in the laboratory on the same diet will ultimately demonstrate similar microbial composition and structure. Therefore, we looked at gut bacteria in Eastern subterranean termite (Reticulitermes flavipes) colonies that were reared in the laboratory with identical diets and rearing conditions. Based on16S rRNA gene sequencing, the observed features, and Shannon’s diversity were significantly different between the colonies while differences in Pielou evenness and Faith phylogenetic diversity were not statistically significant. In addition, the microbial community structures were significantly different between colonies. Based on ANCOM (Analysis of Composition of Microbiomes), the taxa Elizabethkingia (Bacteroidetes: Flavobacteriales) and Chryseobacterium (Bacteroidetes: Flavobacteriales) were differentially abundant between the colonies. These results suggest that providing the exact same diet and rearing environment for >2 yr cannot result in identical gut microbiomes between termite colonies.

A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations

AbstractAimGroundwater harbours an exceptional fauna and provides invaluable ecosystem services, yet is among the least explored and consequently least protected ecosystems. Successful protection of its biodiversity depends on complete species inventories, knowledge of species spatial distribution, and quantification of biodiversity patterns, as well as disentanglement of the processes that shaped biodiversity patterns. We studied the hyper‐speciose amphipod genusNiphargusas a model system within a global subterranean biodiversity hotspot. We linked the biodiversity patterns with possible underlying processes and discuss the needs to include information on different origins of biodiversity into conservation approaches.LocationEurope, Western Balkans.MethodsWe analysed biodiversity patterns ofNiphargususing two biodiversity metrics, species richness and phylogenetic diversity, on a grid‐based approach. To account for high cryptic diversity, we replaced nominal species with taxonomic units identified in unilocus delimitations (MOTUs). We built a time‐calibrated multilocus phylogeny of 512 NiphargusMOTUs from within and outside the study area, and calculated Faith's phylogenetic diversity, standardized effect sizes of phylogenetic diversity, and residual of phylogenetic diversity regressed onto species richness.ResultsWithin the study area, we recognized 245 MOTUs, belonging to differentNiphargusclades. Species richness is highest in a north‐western hotspot, although some species‐rich cells were detected also in the south‐east. High phylogenetic diversity coincides with high species richness in the north‐west, while in the south‐east it is lower than expected.Main conclusionsWe have shown that species richness does not predictably correlate with phylogenetic diversity. This difference suggests that different processes have led to the formation of species‐rich areas in the Western Balkans: through a combination of dispersal and speciation in the north‐west, and local radiation in the south‐east, respectively. This calls for caution in conservation strategies relying solely on number of species and may change the view on conservation priorities within this region.

Fecal and soil microbiota composition of gardening and non-gardening families

Historically, humans have interacted with soils, which contain a rich source of microorganisms. Fruit and vegetable gardening is the primary interaction humans have with soil today. Animal research reveals that soil microorganisms can be transferred to the rodent intestine. However, studies on fecal and soil microbial changes associated with gardening in humans are lacking. The current case-controlled cohort study aimed to characterize the fecal and soil microbiota of gardening families (n = 10) and non-gardening (control) families (n = 9). Families included two adults and one child (5–18 years) for a total of 56 participants. All participants provided a fecal sample, soil sample, and diet history questionnaires before the gardening season (April) and during the peak of the gardening season (August). Healthy Eating Index (HEI-2015) scores and nutrient analysis were performed. Fecal and soil DNA were extracted and amplified. Sequence data were then processed and analyzed. Peak season gardening families tended to have greater fecal operational features, a greater Faith's Phylogenetic Diversity score, greater fiber intake, and higher abundances of fiber fermenting bacteria than peak control families. Soil endemic microbes were also shared with gardening participant’s fecal samples. This study revealed that the fecal microbiota of gardening families differs from non-gardening families, and that there are detectable changes in the fecal microbial community of gardeners and their family members over the course of the gardening season. Additional research is necessary to determine if changes induced by gardening on the gut microbiota contribute to human health.

Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations

BackgroundThe microbiome of the digestive tract exerts fundamental roles in host physiology. Extrinsic factors including lifestyle and diet are widely recognized as key drivers of gut and oral microbiome compositions. Although drinking water is among the food items consumed in the largest amount, little is known about its potential impact on the microbiome. ObjectivesWe explored the associations of plain drinking water source and intake with gut and oral microbiota compositions in a population-based cohort. MethodsMicrobiota, health, lifestyle, and food intake data were extracted from the American Gut Project public database. Associations of drinking water source (bottled, tap, filtered, or well water) and intake with global microbiota composition were evaluated using linear and logistic models adjusted for anthropometric, diet, and lifestyle factors in 3413 and 3794 individuals, respectively (fecal samples; 56% female, median [IQR] age: 48 [36–59] y; median [IQR] BMI: 23.3 [20.9–26.3] kg/m2), and in 283 and 309 individuals, respectively (oral samples). ResultsDrinking water source ranked among the key contributing factors explaining the gut microbiota variation, accounting for 13% [Faith's phylogenetic diversity (Faith's PD)] and 47% (Bray–Curtis dissimilarity) of the age effect size. Drinking water source was associated with differences in gut microbiota signatures, as revealed by β diversity analyses (P < 0.05; Bray–Curtis dissimilarity, weighted UniFrac distance). Subjects drinking mostly well water had higher fecal α diversity (P < 0.05; Faith's PD, observed amplicon sequence variants), higher Dorea, and lower Bacteroides, Odoribacter, and Streptococcus than the other groups. Low water drinkers also exhibited gut microbiota differences compared with high water drinkers (P < 0.05; Bray–Curtis dissimilarity, unweighted UniFrac distance) and a higher abundance of Campylobacter. No associations were found between oral microbiota composition and drinking water consumption. ConclusionsOur results indicate that drinking water may be an important factor in shaping the human gut microbiome and that integrating drinking water source and intake as covariates in future microbiome analyses is warranted.

Spatial distribution of bacterioplankton community composition and their diversity in Lake Fuxian during thermal stratification period

水体垂向分层是深水湖泊一个重要的特征，这不仅影响水体理化环境因子，而且影响水生生物组成的垂向分布，但是对不同水层水体细菌的多样性和群落结构组成的形成与维持机制知之甚少. 本研究以抚仙湖为研究对象，在水体热力分层期间采集不同位点、不同水层水样，借助16S rDNA Illumina Miseq高通量测序技术，探究水体细菌多样性和群落结构组成的空间分布特征及关键影响因子. 研究结果表明：(1)抚仙湖北部湖心在水深15~40 m处出现温跃层，温度由23℃降至15℃，其余理化环境因子也存在明显的垂向分层现象；与垂向差异相比，表层水体各理化因子在水平方向上的差异相对较小. (2)在水平方向上，南部湖心表层水体细菌alpha多样性(Operational Taxonomic Unit数目和Faith's phylogenetic diversity)最高；在垂向上，水体细菌alpha多样性随着采样水深的增加呈现单峰分布，在30和40 m水层最高；水体细菌alpha和beta多样性的垂向差异均显著大于水平方向差异. (3)表层水体细菌主要由Actinomycetales、unidentified Cyanobacteria、Burkholderiales和Sphingobacteriales组成；温跃层中以Pseudomonadales为主；均温层的优势菌群为unidentified Chloroflexi、Actinomycetales和Burkholderiales. 典范对应分析表明溶解性有机碳、溶解氧、硝态氮、氨氮和总磷浓度是影响细菌群落组成的主要环境因子.;Deep lakes are typically characterized by thermal stratification throughout the year, except for a short mixing period in winter. This vertical partitioning has important effects on many biotic, physical and chemical characteristics of the water column. However, at present, little is known about how these changes affect the vertical distribution of bacterioplankton community diversity. In this study, Lake Fuxian with a relatively long thermal stratification period every year, was chosen for the investigation of bacterioplankton distribution, diversity and composition on August 25th, 2013. 16S rDNA Illumina Miseq high-throughput sequencing technology was performed on DNA extracted from water samples collected from different locations and different water depths. The results showed that: (1) A thermocline appeared in the lake center and in the northern part of this lake at the depth of 15-40 m, with the temperature dropping from 23℃ to 15℃. Other physical and chemical factors also showed obvious vertical stratification pattern. Horizontally, there is no significant difference in physicochemical features. (2) In the horizontal direction, the alpha diversities of plankton bacteria (the number of Operational Taxonomic Units and Faith's phylogenetic diversity) in the surface water of the southern lake center was the highest; in the vertical direction, the alpha diversity gradually increased with the increase of the sampling depth, topping at the depths of 30 m or 40 m, and then gradually decreased; the difference of the bacterioplankton alpha and beta diversity in the vertical direction was significantly greater than those in the horizontal direction. (3) The bacterioplankton in the epilimnion were mainly composed of Actinomycetales, unidentified Cyanobacteria, Burkholderiales and Sphingobacteriales; the relative abundance of Pseudomonadales in the thermocline significantly increased and became dominant; unidentified Chloroflexi, Actinomycetales and Burkholderiales were the dominant bacterial taxa in the hypolimnion. The canonical correspondence analysis demonstrated that the concentrations of dissolved organic carbon, dissolved oxygen, nitrate, ammonium and total phosphorus are the significant environmental variables shaping the bacterial community's composition and diversity.

Chronic pancreatitis in a caerulein-induced mouse model is associated with an altered gut microbiome

BackgroundChronic pancreatitis (CP) is an inflammatory disease of the pancreas with loss of exocrine/endocrine functions as well as development of fibrosis. Dysbiosis of gut microbiome has been shown to be involved in the pathogenesis of many disease processes. Therefore, we aim to investigate the alteration in gut microbiome associated with CP in caerulein-induced mouse model. MethodsCP was induced in C57Bl/6 by using caerulein injections (50 μg/kg/h, i.p., x7, twice weekly for 10 weeks). Stool samples were collected either one week after end of injection (10-week CP) or 6 weeks (16-week CP). DNA was extracted from stool samples and V4 region of 16S rDNA was sequenced for microbiome analysis. ResultsCP was strongly associated with the alteration in the composition of the gut microbiome, evidenced by differences in α and β diversity. When β diversity was measured using both weighted and unweighted UniFrac distances, stool from control mice is significantly different from mice on 10-week or 16-week CP (q < 0.01). The α-diversity measured by Faith's phylogenetic diversity was lowest in stool from healthy control and highest in stool from mice with 16-week CP (p < 0.001). Bacteria taxa differentially enriched in CP samples were detected using linear discriminant analysis. Bacteria from genera Bifidobacterium, Akkermansia, and Desulfovibrio were enriched in samples from 10-week CP mice. Bacteria from genera Allobaculum, Prevotella, and Bacteroides were enriched in samples from 16-week CP mice. ConclusionTogether, these analyses reveal pronounced alteration in the gut microbiome composition, diversity, and function when mice develop CP.

Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions.

Commonly used medications produce changes in the gut microbiota, however, the impact of these medications on the composition of the oral microbiota is understudied. Saliva samples were obtained from 846 females and 368 males aged 35-69 years from a Canadian population cohort, the Atlantic Partnership for Tomorrow's Health (PATH). Samples were analyzed by 16S rRNA gene sequencing and differences in microbial community compositions between nonusers, single-, and multi-drug users as well as the 3 most commonly used medications (thyroid hormones, statins, and proton pump inhibitors (PPI)) were examined. Twenty-six percent of participants were taking 1 medication and 21% were reported taking 2 or more medications. Alpha diversity indices of Shannon diversity, Evenness, Richness, and Faith's phylogenetic diversity were similar among groups, likewise beta diversity as measured by Bray-Curtis dissimilarity (R2 = 0.0029, P = 0.053) and weighted UniFrac distances (R2 = 0.0028, P = 0.161) were non-significant although close to our alpha value threshold (P = 0.05). After controlling for covariates (sex, age, BMI), six genera (Saprospiraceae uncultured, Bacillus, Johnsonella, Actinobacillus, Stenotrophomonas, and Mycoplasma) were significantly different from non-medication users. Thyroid hormones, HMG-CoA reductase inhibitors (statins) and PPI were the most reported medications. Shannon diversity differed significantly among those taking no medication and those taking only thyroid hormones, however, there were no significant difference in other measures of alpha- or beta diversity with single thyroid hormone, statin, or PPI use. Compared to participants taking no medications, the relative abundance of eight genera differed significantly in participants taking thyroid hormones, six genera differed in participants taking statins, and no significant differences were observed with participants taking PPI. The results from this study show negligible effect of commonly used medications on microbial diversity and small differences in the relative abundance of specific taxa, suggesting a minimal influence of commonly used medication on the salivary microbiome of individuals living without major chronic conditions.

Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.