Faith's Phylogenetic Diversity Research Articles

Alpha Diversity Indices as Indicators of the Variability of Gut Microbiota in Obese Adolescents of Different Ethnicities.

We compared alpha diversity indices of the intestinal microbiota in adolescents with obesity and normal body weight, taking into account their ethnicity. Intestinal biocenosis was studied by metasequencing of amplicon libraries of V3-V4 fragments of the 16S rRNA gene. The alpha diversity of the microbiota was assessed using classical and alternative indices. Statistically significant differences in intestinal microbiota were observed between Russians with obesity and Buryats with normal body weight, as well as between Russians with obesity and Buryats with obesity when assessing the Shannon-Weaver, Chao1 indices, Faith phylogenetic diversity index, ACE, Fisher, Gini coefficient, Margalef, and Menkhinik indices. It was shown that alpha diversity indices can be used to assess significance of differences and variability of the intestinal microbiota in multifactorial diseases such as obesity in adolescents; however, the scope of application of the criteria should be considered.

Short Communication: Comparing the microbiota diversity from the core, middle part and rind of six Spanish commercial goat cheeses

The cheese core has a lower oxygen saturation and salinity and a higher acidity than the rind, but there is controversy about the incidence of such factors on the magnitude of microbial diversity. The goal of the current work was to investigate the existence of differences in α-diversity between the core, middle part, and rind of six Spanish commercial cheeses through a sequencing approach. To this end, we have collected rind, middle part, and core samples from fresh (H and M), soft semi-ripened (C and P), hard semi-ripened (B) and semi-hard aged (G) goat cheeses. After purifying deoxyribonucleic acid from these 18 samples, the V3-V4 ultravariable region of the 16S rRNA gene was sequenced. The analysis of microbial composition revealed that lactic acid bacteria from the genera Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc are predominant in all six goat cheeses. Furthermore, we identified several psychrophilic taxa often associated with the post-pasteurization contamination of refrigerated milk. Comparison of three α-diversity estimators (Chao1, Shannon and Faith's phylogenetic diversity indices) of microbiota in the core, middle part, and rind of all six goat cheeses did not reveal substantial differences, being only significant (at the nominal level) the comparison of rind vs middle part for the Shannon index (P-value = 0.031). Moreover, the construction of a dendrogram based on Aitchison distances revealed that cheese samples cluster according to their manufacturing characteristics, with a clear distinction between fresh vs semi-ripened or aged cheeses. We conclude that the magnitude of microbial α-diversity in the cheese core is similar to that in the rind despite their different physicochemical attributes. This result could be because physicochemical differences between cheese compartments are often attenuated during cheese ripening.

Anna Karenina as a promoter of microbial diversity in the cosmopolitan agricultural pest Zeugodacus cucurbitae (Diptera, Tephritidae).

Gut microbial communities are critical in determining the evolutive success of fruit fly phytophagous pests (Diptera, Tephritidae), facilitating their adaptation to suboptimal environmental conditions and to plant allelochemical defences. An important source of variation for the microbial diversity of fruit flies is represented by the crop on which larvae are feeding. However, a "crop effect" is not always the main driver of microbial patterns, and it is often observed in combination with other and less obvious processes. In this work, we aim at verifying if environmental stress and, by extension, changing environmental conditions, can promote microbial diversity in Zeugodacus cucurbitae (Coquillett), a cosmopolitan pest of cucurbit crops. With this objective, 16S rRNA metabarcoding was used to test differences in the microbial profiles of wild fly populations in a large experimental setup in Eastern Central Tanzania. The analysis of 2,973 unique ASV, which were assigned to 22 bacterial phyla, 221 families and 590 putative genera, show that microbial α diversity (as estimated by Abundance Coverage Estimator, Faith's Phylogenetic Diversity, Shannon-Weiner and the Inverse Simpson indexes) as well as β microbial diversity (as estimated by Compositional Data analysis of ASVs and of aggregated genera) significantly change as the species gets closer to its altitudinal limits, in farms where pesticides and agrochemicals are used. Most importantly, the multivariate dispersion of microbial patterns is significantly higher in these stressful environmental conditions thus indicating that Anna Karenina effects contribute to the microbial diversity of Z. cucurbitae. The crop effect was comparably weaker and detected as non-consistent changes across the experimental sites. We speculate that the impressive adaptive potential of polyphagous fruit flies is, at least in part, related to the Anna Karenina principle, which promotes stochastic changes in the microbial diversity of fly populations exposed to suboptimal environmental conditions.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems.

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain.

Mountain ecosystems harbor evolutionarily unique and exceptionally rich biodiversity, particularly in insects. In this study, we characterized the diversity, community stability, and assembly mechanisms of butterflies on a subtropical mountain in the Chebaling National Nature Reserve, Guangdong Province, China, using grid-based monitoring across the entire region for two years. The results showed that species richness, abundance, and Faith's phylogenetic diversity decreased with increasing elevation; taxonomic diversity played a considerable role in mediating the effects of environmental changes on stability. Moreover, our results showed that stochastic processes are dominant in governing the assembly of butterfly communities across all elevational gradients, with habitats at an elevation of 416-580 m subjected to the strongest stochastic processes, whereas heterogeneous selection processes displayed stronger effects on the assembly of butterfly communities at 744-908 m, 580-744 m, and 908-1072 m, with abiotic factors inferred as the main driving forces. In addition, significant differences were detected between the barcode tree and the placement tree for the calculated β-NTI values at 416-580 m. Overall, this study provides new insights into the effects of environmental change on the stability and assembly of butterflies in Chebaling, which will be beneficial for biodiversity conservation and policy development.

487 - Adult atopic dermatitis is associated with impaired oral health and oral dysbiosis - a case-control study

Abstract Background Previous studies linked chronic oral diseases to skin disorders such as psoriasis. However, data about oral health and oral microbiota in atopic dermatitis (AD) is sparse. Objectives To compare the oral health status and oral microbiota of AD patients and healthy controls. Methods This was a prospective sex and age- matched case-control study comparing adult participants with and without dermatologist-verified AD. Exclusion criteria included recent use of oral, topical, or systemic medication that could affect oral health or microbiome assessment. Oral health indices including Gingival Index, Plaque Index, Oral Hygiene Index, Caries Severity Index and prosthodontics status, were assessed by a dentist. Samples of oral flora were collected and subjected to high-throughput 16S rRNA gene sequencing analysis for microbiome analysis. Results Forty-five AD participants and 41 non-AD controls were recruited. The two groups had no significant differences in terms of their demographic and clinical characteristics, except for the higher rate of atopic co-morbidities in the AD group (p<.001). Compared to the control group, participants with AD had significantly poorer plaque (p=0.04) and oral hygiene indices (p=0.04) and a trend towards higher gingival index (p=0.05). The results of the Faith phylogenetic diversity (FDR) test indicated that the oral microbial diversity in the AD group was significantly higher (α-diversity, FDR-adjusted p=0.0007) when compared with the control group. Characterization of the similarities and differences in the composition of the microbial communities between the samples (β-diversity) from the AD patients and controls indicated that they clustered separately. The groups showed significant dissimilarity and distinct clustering of microbial abundance (FDR-adjusted p=0.001). Importantly, higher community diversity was previously linked to periodontitis and gingival disease. Furthermore, AD patients had a significantly increased abundance of taxa correlated with oral diseases and decreased abundance of oral health-associated bacteria. Conclusion AD appears to be associated with poorer oral health and oral dysbiosis, and thus, there is a need to increase the awareness of both patients and physicians about oral health.

Gut dysbiosis in patients with chronic pain: a systematic review and meta-analysis.

Recent evidence supports the contribution of gut microbiota dysbiosis to the pathophysiology of rheumatic diseases, neuropathic pain, and neurodegenerative disorders. The bidirectional gut-brain communication network and the occurrence of chronic pain both involve contributions of the autonomic nervous system and the hypothalamic pituitary adrenal axis. Nevertheless, the current understanding of the association between gut microbiota and chronic pain is still not clear. Therefore, the aim of this study is to systematically evaluate the existing knowledge about gut microbiota alterations in chronic pain conditions. Four databases were consulted for this systematic literature review: PubMed, Web of Science, Scopus, and Embase. The Newcastle-Ottawa Scale was used to assess the risk of bias. The study protocol was prospectively registered at the International prospective register of systematic reviews (PROSPERO, CRD42023430115). Alpha-diversity, β-diversity, and relative abundance at different taxonomic levels were summarized qualitatively, and quantitatively if possible. The initial database search identified a total of 3544 unique studies, of which 21 studies were eventually included in the systematic review and 11 in the meta-analysis. Decreases in alpha-diversity were revealed in chronic pain patients compared to controls for several metrics: observed species (SMD= -0.201, 95% CI from -0.04 to -0.36, p=0.01), Shannon index (SMD= -0.27, 95% CI from -0.11 to -0.43, p<0.001), and faith phylogenetic diversity (SMD -0.35, 95% CI from -0.08 to -0.61, p=0.01). Inconsistent results were revealed for beta-diversity. A decrease in the relative abundance of the Lachnospiraceae family, genus Faecalibacterium and Roseburia, and species of Faecalibacterium prausnitzii and Odoribacter splanchnicus, as well as an increase in Eggerthella spp., was revealed in chronic pain patients compared to controls. Indications for gut microbiota dysbiosis were revealed in chronic pain patients, with non-specific disease alterations of microbes. https://www.crd.york.ac.uk/prospero/, identifier CRD42023430115.

Association of oral microbiome with oral human papillomavirus infection: a population study of the National Health and Nutrition Examination Survey, 2009-2012.

Oral human papillomavirus(HPV) infection and the oral microbiome are associated with oropharyngeal cancer. However, population-based data on the association of oral microbiome with oral HPV infection are limited. We performed a cross-sectional analysis of 5,496 participants aged 20-59 in National Health and Nutrition Examination Surveys(NHANES):2009-2012. The association between either oral microbiome alpha diversity or beta diversity and oral HPV infection was assessed using multivariable logistic regression or principal coordinate analyses(PCoA) and multivariate analysis of variance(PERMANOVA). For alpha diversity, we found a lower number of observed Amplicon sequence variants(ASVs) (adjusted odds ratio[aOR] = 0.996; 95%CI = 0.992-0.999) and reduced Faith's Phylogenetic Diversity(aOR = 0.95; 95%CI = 0.90-0.99) associated with high-risk oral HPV infection in the overall population. This trend was observed in males for both high-risk and any oral HPV infection. Beta diversity showed differentiation of oral microbiome community by high-risk oral HPV infection as measured by Bray-Curtis dissimilarity (R2 = 0.054%; P = .029) and unweighted UniFrac distance (R2 = 0.046%; P = .045) among the overall population, and associations were driven by males. Both oral microbiome alpha diversity(within-sample richness and phylogenetic diversity) and beta diversity(heterogeneous dispersion of oral microbiome community) are associated with HPV infection. Longitudinal studies are needed to characterize the role of the microbiome in the natural history of oral HPV infection.

Ocular surface microbiota in patients with varying degrees of dry eye severity.

To elucidate the profiles of commensal bacteria on the ocular surfaces of patients with varying severity of dry eye (DE). The single-center, prospective, case-control, observational study categorized all participants into three distinct groups: 1) control group (n=61), 2) mild DE group (n=56), and 3) moderate-to-severe DE group (n=82). Schirmer's tear secretion strips were used, and the bacterial microbiota was analyzed using 16S ribosomal ribonucleic acid gene sequencing. The three groups had significant differences in alpha diversity: the control group had the highest richness (Chao1, Faith's phylogenetic diversity), the mild DE group showed the highest diversity (Shannon, Simpson), and the moderate-to-severe DE group had the lowest of the above-mentioned indices. DE severity was positively correlated with a reduction in beta diversity of the microbial community, with the moderate-to-severe DE group exhibiting the lowest beta diversity. Linear discriminant analysis effect size presented distinct dominant taxa that significantly differed between each. Furthermore, the exacerbation of DE corresponded with the enrichment of certain pathogenic bacteria, as determined by random forest analysis. As DE severity worsens, microbial community diversity tends to decrease. DE development corresponds with changes in microbial constituents, primarily characterized by reduced microbial diversity and a more homogenous species composition.

Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs (Rana luteiventris) in a montane landscape

The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.

Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng.

The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng. Differential responses of total and active edaphic rhizosphere bacterial communities to continuous cropping of Panax notoginseng.

Dysbiosis of the gut microbiota as a susceptibility factor for Kawasaki disease.

Gut microbial imbalance (dysbiosis) has been reported in patients with acute Kawasaki disease (KD). However, no studies have analyzed the gut microbiota while focusing on susceptibility to KD. This study aimed to evaluate whether dysbiosis elevates susceptibility to KD by assessing children with a history of KD. Fecal DNA was extracted from 26 children with a history of KD approximately 1 year prior (KD group, 12 boys; median age, 32.5 months; median time from onset, 11.5 months) and 57 age-matched healthy controls (HC group, 35 boys; median age, 36.0 months). 16S rRNA gene analysis was conducted with the Illumina Miseq instrument. Sequence reads were analyzed using QIIME2. For alpha diversity, Faith's phylogenetic diversity was significantly higher in the KD group. Regarding beta diversity, the two groups formed significantly different clusters based on Bray-Curtis dissimilarity. Comparing microbial composition at the genus level, the KD and HC groups were significantly different in the abundance of two genera with abundance over 1% after Benjamini-Hochberg false discovery rate correction for multiple comparisons. Compared with the HC group, the KD group had higher relative abundance of Ruminococcus gnavus group and lower relative abundance of Blautia. Ruminococcus gnavus group reportedly includes pro-inflammatory bacteria. In contrast, Blautia suppresses inflammation via butyrate production. In the predictive functional analysis, the proportion of gut microbiota involved in several pathways was lower in the KD group. Therefore, dysbiosis characterized by distinct microbial diversity and decreased abundance of Blautia in parallel with increased abundance of Ruminococcus gnavus group might be a susceptibility factor for KD.

Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure

BackgroundThere is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity. MethodsThis multicenter case–control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances. ResultsShannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE. ConclusionsGut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.

Elexacaftor-tezacaftor-ivacaftor decreases pseudomonas abundance in the sinonasal microbiome in cystic fibrosis.

Chronic rhinosinusitis (CRS) is common in individuals with cystic fibrosis (CF) and is marked by chronic inflammation and episodes of infection that negatively impact quality of life. Several studies have shown that elexacaftor-tezacaftor-ivacaftor (ETI) improves symptoms and examination findings in CF-CRS. The current study determines the effect of ETI on the sinonasal microbiota in CF. Sinonasal samples were collected under endoscopic visualization before and after starting ETI. Samples were subjected to 16S amplicon sequencing and sequences were processed with the QIIME2 pipeline with subsequent analysis using the vegan R-package. Twenty-nine individual baseline samples and 23 sample pairs pre-/post-ETI were available. At baseline, the cohort had samples dominated by Staphylococcus, and alpha diversity was lower than that of a published reference set of individuals without sinonasal disease. Individuals with prior sinus surgery had lower alpha diversity as measured by Shannon Index, Observed Richness, and Faith's phylogenetic diversity Index. Beta diversity differed between individuals with and without allergic rhinitis, with higher Staphylococcus abundance in those with allergic rhinitis. No change in alpha or beta diversity was seen after a median of 9 months on ETI. With ETI, the Pseudomonas genus and the genus containing Burkholderia decreased in samples containing these taxa at baseline. Pseudomonas abundance decreased with treatment as measured by qPCR. Core sinonasal microbiome members Staphylococcus, Corynebacterium, and Streptococcus were unchanged, while Moraxella increased with ETI. Treatment with ETI leads to a reduction in Pseudomonas abundance within the sinonasal microbiome of individuals with Pseudomonas at baseline.

The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal.

The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.

Global variation in the relationship between avian phylogenetic diversity and functional distance is driven by environmental context and constraints

AbstractAimIf evolutionary distance is akin to evolutionary chance, then it follows that species assemblages that are distantly related will also be more disparate in terms of their traits, features and the niches they occupy. Yet, studies have found that the total phylogenetic distance of an assemblage, known as phylogenetic diversity, is an unreliable surrogate for functional diversity. We investigate global variation in the relationship between Faith's phylogenetic diversity (PD) and mean pairwise functional distance (MPFD) across latitude and the influence of migratory species on both these aspects of diversity.LocationGlobal.Time periodPresent day.Major taxa studiedBirds.MethodsWe measure PD and MPFD for over 9000 species of bird across more than 17,000 globally distributed assemblages. We obtain standardised effect sizes for both indices by simulating assemblage composition under an ecologically informed null model. We employ path analysis to characterize variation in the relationship between PD's and MPFD across latitude, elevation and with proportion of migratory species.ResultsGlobally, assemblages that were phylogenetically diverse tended to be less functionally dispersed than expected; however, this relationship showed considerable variation across latitude decreasing with distance from the equator. The proportion of migratory species in an assemblage was found to be an important predictor of functional diversity, with migrant rich assemblages generally showing less functional diversity than expected. We identify the Andes and Hengduan Mountains as regions of exceptional bird functional diversity.Main conclusionsThe relationship between phylogenetic diversity and function diversity is context specific, varying across environmental gradients such as latitude, and influenced by ecological phenomena such as migration. Thus, care should be taken using phylogenetic diversity as a proxy for functional diversity, particularly in clades with sparse functional data. Instead, we recommend that studies consider how phylogenetic diversity's surrogacy for functional diversity may be impacted by environmental context and evaluate empirical observations against biogeographically constrained and ecologically informed null models.

Grazing alters the relationship between alpine meadow biodiversity and ecosystem multifunctionality

The relationship between biodiversity and ecosystem multifunctionality (EMF) depends on changes in environmental disturbance. Plant and soil biological diversity can mediate EMF, but how these change in response to grazing disturbance remains unknown. Here we present an 8-year experiment on sheep grazing control in alpine grasslands in Gannan Tibetan Autonomous Prefecture, Gansu Province, China. Plant species richness, FRic (functional richness), PD (Faith's phylogenetic diversity), soil biological diversity (bacterial, fungal, and ciliate diversity), and multiple ecosystem functions were measured and calculated. The results showed that increasing grazing intensity caused a decrease in biodiversity and EMF and that biodiversity and ecosystem function differed significantly (P < 0.05) between grazing intensities. EMF was positively correlated with species richness, functional diversity, and soil bacterial diversity (P < 0.05), with 23.6 %, 10.8 %, and 12.1 % of EMF explained by changes in grazing intensity, respectively. The interaction terms of grazing intensity, plant species richness, and soil biological diversity were negatively correlated with EMF (P < 0.05). This shift in the relationship between plant or soil biological diversity and EMF occurs at a grazing intensity index of around 0.7, i.e., the impact of plant species richness on EMF is more significant when the grazing intensity index is below 0.67. The effect of soil biological diversity on EMF is more substantial when the grazing intensity index is above 0.86. Conclusion: High grazing intensity directly affects soil bulk density and pH and indirectly affects EMF by regulating plant species richness and soil biological diversity changes. Loss of plant and soil biological diversity can have extreme consequences under low and high grazing intensity disturbance conditions. Therefore, we must develop biodiversity conservation strategies for external disturbances to mitigate the effects of land use practices such as grazing disturbances.

Laxative Abuse Is Associated With a Depleted Gut Microbial Community Structure Among Women and Men With Binge-Eating Disorder or Bulimia Nervosa: The Binge Eating Genetics Initiative.

This study assessed the associations of binge eating, compensatory behaviors, and dietary restraint with the composition and diversity of the intestinal microbiota among participants with binge-eating disorder or bulimia nervosa. We analyzed data from 265 participants aged 18 to 45 years with current binge-eating disorder or bulimia nervosa enrolled in the Binge Eating Genetics Initiative study. We evaluated the associations of binge-eating frequency; presence/absence and frequency of vomiting, laxative use, and compulsive exercise; and dietary restraint with abundances of gut microbial genera, species, and diversity (Shannon diversity, Faith phylogenetic diversity, and Peilou's evenness) from 16S rRNA gene sequencing. General linear regression models adjusted for potential confounders, including age and current body mass index, were used to test associations; p values were corrected for the false discovery rate. The normalized abundance of four genus- and species-level gut microbes and three diversity indices were lower among Binge Eating Genetics Initiative participants who reported any laxative use compared with those who reported no laxative use. Vomiting frequency was positively associated with the normalized abundance of the genus Escherichia-Shigella , a potential pathobiont, although the association was attenuated to nonsignificance after adjustment for age, body mass index, and binge-eating episodes. Laxative use was highly and uniformly predictive of a reduced gut microbial diversity including potential commensals and pathobionts, and should be assessed and accounted for in all future studies of eating disorders and the gut microbiota. Future studies should collect data on specific medications-particularly laxatives-and dietary intake to obtain unbiased estimates of the effect of eating disorders on the gut microbiota and identify potential downstream clinical implications.Trial Registration:ClinicalTrials.gov identifier: NCT04162574 .

The photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean.

The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi- and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny-based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0-1,000 m) at the Bermuda Atlantic Time-series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha-diversity (based on Faith's phylogenetic diversity index) from surface to 1,000-m waters. Second, multivariate analyses of beta-diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade-level correlations (EPA-ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti-correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha-diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with prevalence of algivory and mixotrophy versus omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.

Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils.

This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were Actinobacteria (32.3%), Proteobacteria (24.8%), Firmicutes (20.7%), Bacteroidetes (6.3%), and Chloroflexi (3.6%), though individual soils varied widely in the relative abundances of these and other phyla. Alpha diversity measured using feature richness (operational taxonomic units [OTUs]), Shannon's entropy, and Faith's phylogenetic diversity (PD) varied significantly between habitats (P = 0.016, P = 0.016, and P = 0.015, respectively). Sand, clay, and silt were significantly correlated with microbial diversity. Highly significant negative correlations were also seen at the class level between both classes Actinobacteria and Thermoleophilia (phylum Actinobacteria) and total sodium (R = -0.82 and P = 0.001 and R = -0.86, P = 0.000, respectively) and slowly available sodium (R = -0.81 and P = 0.001 and R = -0.8 and P = 0.002, respectively). Additionally, class Actinobacteria also showed significant negative correlation with sodium/calcium ratio (R = -0.81 and P = 0.001). More work is needed to understand if there is a causal relationship between these soil chemical parameters and the relative abundances of these bacteria. IMPORTANCE Soil microbes perform a multitude of essential biological functions, including organic matter decomposition, nutrient cycling, and soil structure preservation. Qatar is one of the most hostile and fragile arid environments on earth and is expected to face a disproportionate impact of climate change in the coming years. Thus, it is critical to establish a baseline understanding of microbial community composition and to assess how soil edaphic factors correlate with microbial community composition in this region. Although some previous studies have quantified culturable microbes in specific Qatari habitats, this approach has serious limitations, as in environmental samples, approximately only 0.5% of cells are culturable. Hence, this method vastly underestimates natural diversity within these habitats. Our study is the first to systematically characterize the chemistry and total microbiota associated with different habitats present in the State of Qatar.