Fifteen forms of biodiversity trend in the Anthropocene

Humans are transforming the biosphere in unprecedented ways, raising the important question of how these impacts are changing biodiversity. Here we argue that our understanding of biodiversity trends in the Anthropocene, and our ability to protect the natural world, is impeded by a failure to consider different types of biodiversity measured at different spatial scales. We propose that ecologists should recognize and assess 15 distinct categories of biodiversity trend. We summarize what is known about each of these 15 categories, identify major gaps in our current knowledge, and recommend the next steps required for better understanding of trends in biodiversity.

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China

Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis.

Several scales of biodiversity affect ecosystem multifunctionality

Society values landscapes that reliably provide many ecosystem functions. As the study of ecosystem functioning expands to include more locations, time spans, and functions, the functional importance of individual species is becoming more apparent. However, the functional importance of individual species does not necessarily translate to the functional importance of biodiversity measured in whole communities of interacting species. Furthermore, ecological diversity at scales larger than neighborhood species richness could also influence the provision of multiple functions over extended time scales. We created experimental landscapes based on whole communities from the world's longest running biodiversity-functioning field experiment to investigate how local species richness (α diversity), distinctness among communities (β diversity), and larger scale species richness (γ diversity) affected eight ecosystem functions over 10 y. Using both threshold-based and unique multifunctionality metrics, we found that α diversity had strong positive effects on most individual functions and multifunctionality, and that positive effects of β and γ diversity emerged only when multiple functions were considered simultaneously. Higher β diversity also reduced the variability in multifunctionality. Thus, in addition to conserving important species, maintaining ecosystem multifunctionality will require diverse landscape mosaics of diverse communities.

Phosphorus limitation, soil-borne pathogens and the coexistence of plant species in hyperdiverse forests and shrublands

Hyperdiverse forests occur in the lowland tropics, whereas the most species-rich shrublands are found in regions such as south-western Australia (kwongan) and South Africa (fynbos). Despite large differences, these ecosystems share an important characteristic: their soils are strongly weathered and phosphorus (P) is a key growth-limiting nutrient. Soil-borne pathogens are increasingly being recognized as drivers of plant diversity in lowland tropical rainforests, but have received little attention in species-rich shrublands. We suggest a trade-off in which the species most proficient at acquiring P have ephemeral roots that are particularly susceptible to soil-borne pathogens. This could equalize out the differences in competitive ability among co-occurring species in these ecosystems, thus contributing to coexistence. Moreover, effective protection against soil-borne pathogens by ectomycorrhizal (ECM) fungi might explain the occurrence of monodominant stands of ECM trees and shrubs amongst otherwise species-rich communities. We identify gaps in our knowledge which need to be filled in order to evaluate a possible link between P limitation, fine root traits, soil-borne pathogens and local plant species diversity. Such a link may help to explain how numerous plant species can coexist in hyperdiverse rainforests and shrublands, and, conversely, how monodominant stands can develop in these ecosystems.

On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community composition is estimated. There is a need for the extension and development of analytic methods for longitudinal microbiota studies. In this paper, we discuss different approaches to model alpha and beta diversity indices in longitudinal microbiota studies and provide both a review of current approaches and a proposal for new methods.

Headwaters are critical reservoirs of microbial diversity for fluvial networks

Streams and rivers form conspicuous networks on the Earth and are among nature's most effective integrators. Their dendritic structure reaches into the terrestrial landscape and accumulates water and sediment en route from abundant headwater streams to a single river mouth. The prevailing view over the last decades has been that biological diversity also accumulates downstream. Here, we show that this pattern does not hold for fluvial biofilms, which are the dominant mode of microbial life in streams and rivers and which fulfil critical ecosystem functions therein. Using 454 pyrosequencing on benthic biofilms from 114 streams, we found that microbial diversity decreased from headwaters downstream and especially at confluences. We suggest that the local environment and biotic interactions may modify the influence of metacommunity connectivity on local biofilm biodiversity throughout the network. In addition, there was a high degree of variability in species composition among headwater streams that could not be explained by geographical distance between catchments. This suggests that the dendritic nature of fluvial networks constrains the distributional patterns of microbial diversity similar to that of animals. Our observations highlight the contributions that headwaters make in the maintenance of microbial biodiversity in fluvial networks.

Diet Diversity Is Associated with Beta but not Alpha Diversity of Pika Gut Microbiota

Wild mammals often consume different food sources as they become geographical available. This change in diet composition is likely to influence the gut microbial community, yet it remains unclear what the relationship looks like—particularly in small herbivores—under natural conditions. We used DNA sequencing approaches to characterize the diet composition and gut microbial community of wild plateau pikas (Ochotona curzoniae) collected from three altitudes. We tested if diet and gut microbiota composition changes across altitudes, and the relationship between diet diversity and gut microbiota diversity. Our results showed that altitude significantly influences the composition of diet and gut microbial communities. Notably, the alpha diversity (Shannon diversity and observed OTUs) of individual diet was not significantly correlated with that of gut microbiota, whereas the beta diversity (Jaccard and Bray-Curtis dissimilarity) of diet was positively correlated with that of gut microbiota. Our study is the first time to highlight the relationship between diet and gut microbiota composition in wild pikas on the Qinghai-Tibet Plateau. It suggests that the species richness within individual gut microbiota does not linearly increase with diet diversity, whereas those individuals that are more similar in diet composition harbor more similar gut microbiota.

Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study

The composition of the diet (what we eat) has been widely related to the microbiota profile. However, whether the timing of food consumption (when we eat) influences microbiota in humans is unknown. A randomized, crossover study was performed in 10 healthy normal-weight young women to test the effect of the timing of food intake on the human microbiota in the saliva and fecal samples. More specifically, to determine whether eating late alters daily rhythms of human salivary microbiota, we interrogated salivary microbiota in samples obtained at 4 specific time points over 24 h, to achieve a better understanding of the relationship between food timing and metabolic alterations in humans. Results revealed significant diurnal rhythms in salivary diversity and bacterial relative abundance ( i.e., TM7 and Fusobacteria) across both early and late eating conditions. More importantly, meal timing affected diurnal rhythms in diversity of salivary microbiota toward an inverted rhythm between the eating conditions, and eating late increased the number of putative proinflammatory taxa, showing a diurnal rhythm in the saliva. In a randomized, crossover study, we showed for the first time the impact of the timing of food intake on human salivary microbiota. Eating the main meal late inverts the daily rhythm of salivary microbiota diversity which may have a deleterious effect on the metabolism of the host.-Collado, M. C., Engen, P. A., Bandín, C., Cabrera-Rubio, R., Voigt, R. M., Green, S. J., Naqib, A., Keshavarzian, A., Scheer, F. A. J. L., Garaulet, M. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study.

Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls

BACKGROUND & AIMS

The importance of the intestinal microbiota for the onset and clinical course of many diseases, including liver diseases like non-alcoholic steatohepatitis and cirrhosis, is increasingly recognized. However, the role of intestinal microbiota in chronic hepatitis C virus (HCV) infection remains unclear.

METHODS

In a cross-sectional approach, the intestinal microbiota of 95 patients chronically infected with HCV (n=57 without cirrhosis [NO-CIR]; n=38 with cirrhosis [CIR]) and 50 healthy controls (HC) without documented liver diseases was analysed.

RESULTS

Alpha diversity, measured by number of phylotypes (S) and Shannon diversity index (H'), decreased significantly from HC to NO-CIR to CIR. S and H' correlated negatively with liver elastography. Analysis of similarities revealed highly statistically significant differences in the microbial communities between HC, NO-CIR and CIR (R=.090; P<1.0×10^-6 ). Stratifying for HCV genotypes even increased the differences. In addition, we observed distinct patterns in the relative abundance of genera being either positive or negative correlated with diseases status.

CONCLUSIONS

This study shows that not only the stage of liver disease but also HCV infection is associated with a reduced alpha diversity and different microbial community patterns. These differences might be caused by direct interactions between HCV and the microbiota or indirect interactions facilitated by the immune system.

Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

Shift in skin microbiota of Western European women across aging

AIMS

The objective of our study was to compare the microbiota diversity between two different age groups of Western European women.

METHODS AND RESULTS

Skin-swab samples were collected directly on the forehead of 34 healthy Western European women: 17 younger (21-31 years old) and 17 older individuals (54-69 years old). Bacterial communities were evaluated using the 16S rRNA gene sequencing. Data revealed a higher alpha diversity on the skin of older individuals compared with younger ones. Overall microbiota structure was different between the two age groups, as demonstrated by beta diversity analysis, which also highlighted a high interpersonal variation within older individuals. Furthermore, taxonomic composition analysis showed both an increase in Proteobacteria and a decrease in Actinobacteria on the older skin. At the genus level, older skin exhibited a significant increase in Corynebacterium and a decrease in Propionibacterium relative abundance.

CONCLUSIONS

Our study revealed a shift in the distribution of skin microbiota during chronological aging in Western European women.

SIGNIFICANCE AND IMPACT OF STUDY

Altogether these results could become the basis to develop new approaches aiming to rebalance the skin microbiota, which is modified during the aging process.

Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease

Background: Gut microbiota are considered to be intrinsic regulators of thyroid autoimmunity. We designed a cross-sectional study to examine the makeup and metabolic function of microbiota in Graves' disease (GD) patients, with the ultimate aim of offering new perspectives on the diagnosis and treatment of GD. Methods: The 16S ribosomal RNA (rRNA) V3-V4 DNA regions of microbiota were obtained from fecal samples collected from 45 GD patients and 59 controls. Microbial differences between the two groups were subsequently analyzed based on high-throughput sequencing. Results: Compared with controls, GD patients had reduced alpha diversity (p < 0.05). At the phylum level, GD patients had a significantly lower proportion of Firmicutes (p = 0.008) and a significantly higher proportion of Bacteroidetes (p = 0.002) compared with the controls. At the genus level, GD patients had greater numbers of Bacteroides and Lactobacillus, although fewer Blautia, [Eubacterium]_hallii_group, Anaerostipes, Collinsella, Dorea, unclassified_f_Peptostreptococcaceae, and [Ruminococcus]_torques_group than controls (all p < 0.05). Subgroup analysis of GD patients revealed that Lactobacillus may play a key role in the pathogenesis of autoimmune thyroid diseases. Nine distinct genera showed significant correlations with certain thyroid function tests. Functional prediction revealed that Blautia may be an important microbe in certain metabolic pathways that occur in the hyperthyroid state. In addition, linear discriminant analysis (LDA) and effect size (LEfSe) analysis showed that there were significant differences in the levels of 18 genera between GD patients and controls (LDA >3.0, all p < 0.05). A diagnostic model using the top nine genera had an area under the curve of 0.8109 [confidence interval: 0.7274-0.8945]. Conclusions: Intestinal microbiota are different in GD patients. The microbiota we identified offer an alternative noninvasive diagnostic methodology for GD. Microbiota may also play a role in thyroid autoimmunity, and future research is needed to further elucidate the role.

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards

Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.

Association of dietary patterns with the gut microbiota in older, community-dwelling men

BACKGROUND

While the gut microbiota is relatively stable through adulthood, its composition is influenced by various host and environmental factors, including changes in health, gastrointestinal processes (e.g., transit time, gastric acidity), medication use, and diet. The association of habitual diet, in the form of a posteriori-derived dietary patterns, and microbiota composition has not been adequately studied, particularly in older men.

OBJECTIVE

The objective was to investigate the association of dietary patterns with the composition and diversity of the gut bacterial microbiota in community-dwelling, older men.

METHODS

This cross-sectional study included 517 men who were participants in the Osteoporotic Fractures in Men (MrOS) Study (≥65 y of age at baseline in 2000-2002) and who provided a stool sample and completed an FFQ at MrOS Visit 4 in 2014-2016. Dietary patterns were derived by factor analysis. 16S ribosomal RNA target gene sequencing was performed and taxonomy assignments were derived using the Greengenes database. Linear regression and permutational multivariate analysis of variance (PERMANOVA) considered variations in alpha and beta diversity by dietary pattern, and a model that implements a 0-inflated Gaussian distribution of mean group abundance for each taxa (metagenomeSeq) assessed taxonomic variations by dietary pattern.

RESULTS

In multivariable-adjusted models, greater adherence to the Western pattern was positively associated with families Mogibacteriaceae and Veillonellaceae and genera Alistipes, Anaerotruncus, CC-115, Collinsella, Coprobacillus, Desulfovibrio, Dorea, Eubacterium, and Ruminococcus, while greater adherence to the prudent pattern was positively associated with order Streptophyta, family Victivallaceae, and genera Cetobacterium, Clostridium, Faecalibacterium, Lachnospira, Paraprevotella, and Veillonella. The relative abundance of the dominant gut bacterial phyla, Bacteroidetes and Firmicutes, did not differ between participants with greater adherence to the Western pattern, compared with those with greater adherence to the prudent pattern. Dietary patterns were not associated with measures of alpha diversity, but beta diversity measures were significantly associated with both Western and prudent patterns.

CONCLUSIONS

We observed significant associations between dietary patterns and measures of gut microbial composition in this sample of community-dwelling, older men.

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's ρ  > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose-built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

Changes in the human gut microbiota composition caused by Helicobacter pylori eradication therapy: A systematic review and meta-analysis

BACKGROUND

The short-term and long-term effect of Helicobacter pylori (H pylori) eradication on the gut microbiota is controversial; hence, this study aimed to clarify changes in the gut microbiome and microbial diversity after H pylori eradication.

MATERIALS AND METHODS

Articles published in PubMed, MEDLINE, and EMBASE were searched up to March 20, 2020, with English-language restriction. The outcomes including gut microbiota and alpha diversity were extracted to analysis. And then, Review Manager 5.3 software was used to conduct the data analysis.

RESULTS

At phylum level, next-generation sequencing was performed. Meta-analysis results showed that Actinobacteria decreased compared with baseline throughout the follow-up period. Proteobacteria increased during short-term follow-up and then returned to normal. In addition, Bacteroidetes decreased and Firmicutes increased only during long-term follow-up. At family or genus level, conventional microbiological culturing was performed. Enterobacteriaceae and Enterococcus both increased during the short-term and interim follow-up. In addition, Lactobacillus only showed a decreasing trend during short-term follow-up, but it appeared statistical decreasing during interim follow-up. Moreover, relatively sufficient evidence showed that alpha diversity decreased during short-term follow-up, and no reliable data were obtained to confirm the change of alpha diversity during interim and long-term follow-up.

CONCLUSION

In different follow-up periods after H pylori eradication, changes in gut microbiota were inconsistent. Microbial diversity decreased in the short-term follow-up, while there was no data to confirm subsequent alterations. The results provided a basis for the rational selection of probiotics in the eradication process. However, further studies are needed to obtain more clues.

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North–West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2–3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.

Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences

BACKGROUND

We conducted a pilot study of reproducibility and associations of microbial diversity and composition in faecal microbial DNA.

METHODS AND RESULTS

Participants (25 men and 26 women, aged 17-65 years) provided questionnaire data and multiple samples of one stool collected with two Polymedco and two Sarstedt devices preloaded with RNAlater. 16S rRNA genes in each faecal DNA aliquot were amplified, sequenced (Roche/454 Life Sciences) and assigned to taxa. Devices were compared for ease of use and reproducibility [intraclass correlation coefficient (ICC)] between duplicate aliquots on diversity and taxonomic assignment. Associations were tested by linear regression. Both collection devices were easy to use. Both alpha diversity (Shannon index) and beta diversity (UniFrac) were higher between than within duplicates (P ≤ 10(-8) ) and did not differ significantly by device (P ≥ 0·62). Reproducibility was good (ICC≥0·77) for alpha diversity and taxonomic assignment to the most abundant phyla, Firmicutes and Bacteroidetes (71·5% and 25·0% of sequences, respectively), but reproducibility was low (ICC≤0·48) for less abundant taxa. Alpha diversity was lower with nonantibiotic prescription medication (P = 0·02), with younger age (P = 0·03) and marginally with higher body mass index (P = 0·08).

CONCLUSIONS

With sampling from various parts of a stool, both devices provided good reproducibility on overall microbial diversity and classification for the major phyla, but not for minor phyla. Implementation of these methods should provide insights into how broad microbial parameters, but not necessarily rare microbes, affect risk of various conditions.

Dahlin K, Latimer AM, Wilson AM, Grady JM, Ollinger SV, Finley AO. Towards connecting biodiversity and geodiversity across scales with satellite remote sensing

ISSUE

Geodiversity (i.e., the variation in Earth's abiotic processes and features) has strong effects on biodiversity patterns. However, major gaps remain in our understanding of how relationships between biodiversity and geodiversity vary over space and time. Biodiversity data are globally sparse and concentrated in particular regions. In contrast, many forms of geodiversity can be measured continuously across the globe with satellite remote sensing. Satellite remote sensing directly measures environmental variables with grain sizes as small as tens of metres and can therefore elucidate biodiversity-geodiversity relationships across scales.

EVIDENCE

We show how one important geodiversity variable, elevation, relates to alpha, beta and gamma taxonomic diversity of trees across spatial scales. We use elevation from NASA's Shuttle Radar Topography Mission (SRTM) and c. 16,000 Forest Inventory and Analysis plots to quantify spatial scaling relationships between biodiversity and geodiversity with generalized linear models (for alpha and gamma diversity) and beta regression (for beta diversity) across five spatial grains ranging from 5 to 100 km. We illustrate different relationships depending on the form of diversity; beta and gamma diversity show the strongest relationship with variation in elevation.

CONCLUSION

With the onset of climate change, it is more important than ever to examine geodiversity for its potential to foster biodiversity. Widely available satellite remotely sensed geodiversity data offer an important and expanding suite of measurements for understanding and predicting changes in different forms of biodiversity across scales. Interdisciplinary research teams spanning biodiversity, geoscience and remote sensing are well poised to advance understanding of biodiversity-geodiversity relationships across scales and guide the conservation of nature.

Gut Microbiome of the Canadian Arctic Inuit

Diet is a major determinant of community composition in the human gut microbiome, and "traditional" diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome. We used deep sequencing of the 16S rRNA gene to compare the gut microbiomes of Montrealers with a Western diet to those of the Inuit consuming a range of traditional and Western diets. At the overall microbial community level, the gut microbiomes of Montrealers and Inuit were indistinguishable and contained similar levels of microbial diversity. However, we observed significant differences in the relative abundances of certain microbial taxa down to the subgenus level using oligotyping. For example, Prevotella spp., which have been previously associated with high-fiber diets, were enriched in Montrealers and among the Inuit consuming a Western diet. The gut microbiomes of Inuit consuming a traditional diet also had significantly less genetic diversity within the Prevotella genus, suggesting that a low-fiber diet might not only select against Prevotella but also reduce its diversity. Other microbes, such as Akkermansia, were associated with geography as well as diet, suggesting limited dispersal to the Arctic. Our report provides a snapshot of the Inuit microbiome as Western-like in overall community structure but distinct in the relative abundances and diversity of certain genera and strains. IMPORTANCE Non-Western populations have been shown to have distinct gut microbial communities shaped by traditional diets. The hitherto-uncharacterized microbiome of the Inuit may help us to better understand health risks specific to this population such as diabetes and obesity, which increase in prevalence as many Inuit transition to a Western diet. Here we show that even Inuit consuming a mostly traditional diet have a broadly Western-like microbiome. This suggests that similarities between the Inuit diet and the Western diet (low fiber, high fat) may lead to a convergence of community structures and diversity. However, certain species and strains of microbes have significantly different levels of abundance and diversity in the Inuit, possibly driven by differences in diet. Furthermore, the Inuit diet provides an exception to the correlation between traditional diets and high microbial diversity, potentially due to their transitioning diet. Knowledge of the Inuit microbiome may provide future resources for interventions and conservation of Inuit heritage.

The mean and variance of phylogenetic diversity under rarefaction

Phylogenetic diversity (PD) depends on sampling depth, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD.We have derived exact formulae for the mean and variance of PD under rarefaction. We confirm that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome.There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance.Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve.The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.

Mediation Analysis as a Means of Identifying Dietary Components That Differentially Affect the Fecal Microbiota of Infants Weaned by Modified Baby-Led and Traditional Approaches

The introduction of "solids" (i.e., complementary foods) to the milk-only diet in early infancy affects the development of the gut microbiota. The aim of this study was to determine whether a "baby-led" approach to complementary feeding that encourages the early introduction of an adult-type diet results in alterations of the gut microbiota composition compared to traditional spoon-feeding. The Baby-Led Introduction to SolidS (BLISS) study randomized 206 infants to BLISS (a modified version of baby-led weaning [BLW], the introduction of solids at 6 months of age, followed by self-feeding of family foods) or control (traditional spoon-feeding of purées) groups. Fecal microbiotas and 3-day weighed-diet records were analyzed for a subset of 74 infants at 7 and 12 months of age. The composition of the microbiota was determined by sequencing of 16S rRNA genes amplified by PCR from bulk DNA extracted from feces. Diet records were used to estimate food and dietary fiber intake. Alpha diversity (number of operational taxonomic units [OTUs]) was significantly lower in BLISS infants at 12 months of age (difference [95% confidence interval {CI}] of 31 OTUs [3.4 to 58.5]; P = 0.028), and while there were no significant differences between control and BLISS infants in relative abundances of Bifidobacteriaceae, Enterobacteriaceae, Veillonellaceae, Bacteroidaceae, Erysipelotrichaceae, Lachnospiraceae, or Ruminococcaceae at 7 or 12 months of age, OTUs representing the genus Roseburia were less prevalent in BLISS microbiotas at 12 months. Mediation models demonstrated that the intake of "fruit and vegetables" and "dietary fiber" explained 29% and 25%, respectively, of the relationship between group (BLISS versus control) and alpha diversity.IMPORTANCE The introduction of solid foods (complementary feeding or weaning) to infants leads to more-complex compositions of microbial communities (microbiota or microbiome) in the gut. In baby-led weaning (BLW), infants are given only finger foods that they can pick up and feed themselves-there is no parental spoon-feeding of puréed baby foods-and infants are encouraged to eat family meals. BLW is a new approach to infant feeding that is increasing in popularity in the United States, New Zealand, the United Kingdom, and Canada. We used mediation modeling, commonly used in health research but not in microbiota studies until now, to identify particular dietary components that affected the development of the infant gut microbiota.

Cecal versus fecal microbiota in Ossabaw swine and implications for obesity

The gut microbiome plays a critical role in the onset and progression of obesity and the metabolic syndrome. However, it is not well documented whether the cecal vs. the fecal microbiome is more relevant when assessing their contributions to these diseases. Here, we amplified the V4 region of the 16S rRNA gene from cecal and fecal samples of female Ossabaw swine fed a low-fat control diet (10.5% fat, n = 4) or Western diet (43.0% fat, 17.8% high fructose corn syrup, 2% cholesterol; n = 3) for 36 wk. Obesity significantly lowered alpha-diversity ( P < 0.05), and there was clear separation in beta-diversity between lean and obese pigs, as well as between cecal and fecal samples ( P < 0.05). Obesity dramatically increased ( P < 0.05) the Firmicutes:Bacteroidetes ratio in fecal samples, and Actinobacteria was higher ( P < 0.05) in fecal vs. cecal samples in obese pigs. Cyanobacteria, Proteobacteria, and Fusobacteria were increased ( P < 0.05), while Spirochaetes, Tenericutes, and Verrucomicrobia were decreased ( P < 0.05) in obese vs. lean pigs. Prevotellaceae was reduced ( P < 0.05) in obese fecal vs. cecal samples. Moreover, cecal samples in obese had greater ( P < 0.05) predicted metabolic capacity for glycan biosynthesis and metabolism and LPS biosynthesis compared with fecal. Obese pigs also had greater ( P < 0.05) capacity for carbohydrate metabolism, which was driven by obese fecal rather than cecal samples and was opposite in lean pigs ( P < 0.05). The observed differences in pro-inflammatory microbiota and their metabolic capacity in cecal vs. fecal samples of obese pigs provide new insight into evaluating the microbiome in the pathogenesis of obesity and metabolic disease.

Symbiont community diversity is more variable in corals that respond poorly to stress

Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts-the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four 'best performer' coral genets were analyzed at the end of the experiment because they survived high temperature, high pCO2 , bacterial exposure, or combined stressors, whereas four 'worst performer' genets were characterized because they experienced substantial mortality under these stressors. At the end of the experiment, seven of eight coral genets mainly hosted Cladocopium symbionts, whereas the eighth genet was dominated by both Cladocopium and Durusdinium symbionts. Symbiodiniaceae alpha and beta diversity were higher in worst performing genets than in best performing genets. Symbiont communities in worst performers also differed more after stress exposure relative to their controls (based on normalized proportional differences in beta diversity), than did best performers. A generalized joint attribute model estimated the influence of host genet and treatment on Symbiodiniaceae community composition and identified strong associations among particular symbionts and host genet performance, as well as weaker associations with treatment. Although dominant symbiont physiology and function contribute to host performance, these findings emphasize the importance of symbiont community diversity and stochasticity as components of host performance. Our findings also suggest that symbiont community diversity metrics may function as indicators of resilience and have potential applications in diverse disciplines from climate change adaptation to agriculture and medicine.