Rethinking "enterotypes"

Effect of chronic and acute heat challenges on fecal microbiota composition, production, and thermoregulation traits in growing pigs1,2

The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

Prevotella Abundance Predicts Weight Loss Success in Healthy, Overweight Adults Consuming a Whole-Grain Diet Ad Libitum: A Post Hoc Analysis of a 6-Wk Randomized Controlled Trial

BACKGROUND

The key to effective weight loss may be to match diet and gut microbes, since recent studies have found that subjects with high Prevotella abundances in their gut microbiota lose more weight on diets rich in fiber than subjects with low Prevotella abundances.

OBJECTIVES

We reanalyzed a 6-wk, parallel, randomized trial to investigate difference in body weight changes when participants, stratified by fecal microbiota composition, consumed ad libitum a whole-grain (WG) or a refined-wheat (RW) diet.

METHODS

We stratified 46 (19 men, 27 women; ages 30-65 y) healthy, overweight adults by baseline Prevotella-to-Bacteroides ratios and Prevotella abundances. Subjects with no Prevotella were analyzed separately (n = 24). Compared with the RW diet (mean = 221 g/d), the WG diet (mean = 228 g/d) had a higher fiber content (33 g/d compared with 23 g/d). Linear mixed models and correlations were applied to link 6-wk changes in body weights and metabolic and microbiota markers, according to Prevotella groups and diets.

RESULTS

The Prevotella abundances correlated inversely with weight changes (r = -0.34; P = 0.043). Consequently, subjects with high Prevotella abundances (n = 15) spontaneously lost 1.80 kg (95% CI: -3.23, -0.37 kg; P = 0.013) more on the WG diet than on the RW diet, whereas those with low Prevotella abundances (n = 31) were weight stable (-0.22 kg; 95% CI: -1.40, 0.96 kg; P = 0.72). Thus, the mean difference between the Prevotella groups was 2.02 kg (95% CI: -3.87, -0.17 kg; P = 0.032). Subjects with no Prevotella lost 1.59 kg (95% CI: -2.65, -0.52 kg; P = 0.004) more on the WG diet than on the RW diet. No 6-wk changes in appetite sensations, glucose metabolisms, or fecal SCFAs were associated with the Prevotella groups.

CONCLUSIONS

Healthy, overweight adults with high Prevotella abundances lost more weight than subjects with low Prevotella abundances when consuming a diet rich in WG and fiber ad libitum for 6 wk. This further supports enterotypes as a potential biomarker in personalized nutrition for obesity management. This t rial was registered at clinicaltrials.gov as NCT02358122.

Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

The present study aimed at investigating the evolution of pigs’ fecal microbiota composition from post-weaning to finishing in a longitudinal analysis. The experiment was conducted on 160 Pietrain × (Large White × Landrace) castrated male and female pigs in two replicates. Feces were collected at 52, 99, 119, 140, and 154 days of age for further 16S rRNA sequencing to analyze the microbiota composition. Pig microbiota evolved strongly from 52 to 99 days of age with an increased abundance of Streptococcaceae and a decreased abundance of Lactobacillaceae. During the finishing stage, microbiota kept evolving at a slower rate. To link the community structure to the performances, the fecal samples were clustered into enterotypes sharing a similar bacterial composition. At 52 days, two enterotypes dominated either by Lactobacillus or by Prevotella–Sarcina were identified. They differed from the two enterotypes determined from 99 to 154 days which were dominated either by Lactobacillus or by Turicibacter–Clostridiumsensustricto. During this time period, 75% of the pigs switched enterotypes. The enterotypes were not related to differences in the overall growth or feeding performance. The enterotype definition was time-dependent and seemed to be related to the sex type at 99 days of age.

Oral microbiome diversity in chimpanzees from Gombe National Park

Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.

The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models-Part I: Overview of Current Methods

Health care is increasingly focused on health at the individual level. In the rapidly evolving field of precision nutrition, researchers aim to identify how genetics, epigenetics, and the microbiome interact to shape an individual's response to diet. With this understanding, personalized responses can be predicted and dietary advice can be tailored to the individual. With the integration of these complex sources of data, an important aspect of precision nutrition research is the methodology used for studying interindividual variability in response to diet. This article stands as the first in a 2-part review of current research investigating the contribution of the gut microbiota to interindividual variability in response to diet. Part I reviews the methods used by researchers to design and carry out such studies as well as the statistical and bioinformatic methods used to analyze results. Part II reviews the findings of these studies, discusses gaps in our current knowledge, and summarizes directions for future research. Taken together, these reviews summarize the current state of knowledge and provide a foundation for future research on the role of the gut microbiome in precision nutrition.

The Microbiota-Gut-Brain Axis

The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-related, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been paramount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.

Microbiota and mucosal defense in IBD: an update

Introduction: Inflammatory bowel diseases (IBD) are on the rise worldwide. This review covers the current concepts of the etiology of Crohn´s disease and ulcerative colitis by focusing on an unbalanced interaction between the intestinal microbiota and the mucosal barrier. Understanding these issues is of paramount importance for the development of targeted therapies aiming at the disease cause.Area covered: Gut microbiota alterations and a dysfunctional intestinal mucosa are associated with IBD. Here we focus on specific defense structures of the mucosal barrier, namely antimicrobial peptides and the mucus layer, which keep the gut microbiota at a distance under healthy conditions and are defective in IBD.Expert commentary: The microbiology of both forms of IBD is different but characterized by a reduced bacterial diversity and richness. Abundance of certain bacterial species is altered, and the compositional changes are related to disease activity. In IBD the mucus layer above the epithelium is contaminated by bacteria and the immune reaction is dominated by the antibacterial response. Human genetics suggest that many of the basic deficiencies in the mucosal response, due to Paneth cell, defensin and mucus defects, are primary. Nutrition may also be important but so far there is no therapy targeting the mucosal barrier.

pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis

MOTIVATION

The human microbiome is notoriously variable across individuals, with a wide range of 'healthy' microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.

RESULTS

We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets.

AVAILABILITY AND IMPLEMENTATION

The R package pldist is available on GitHub at https://github.com/aplantin/pldist.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Relationship between the gut microbiome and brain function

It has become increasingly evident in recent years that the gut microbiome and the brain communicate in a bidirectional manner, with each possibly affecting the other's functions. Substantial research has aimed to understand the mechanisms of this interaction and to outline strategies for preventing or treating nervous system-related disturbances. This review explores the evidence demonstrating how the gut microbiome may affect brain function in adults, thereby having an impact on stress, anxiety, depression, and cognition. In vitro, in vivo, and human studies reporting an association between a change in the gut microbiome and functional changes in the brain are highlighted, as are studies outlining the mechanisms by which the brain affects the microbiome and the gastrointestinal tract. Possible modes of action to explain how the gut microbiome and the brain functionally affect each other are proposed. Supplemental probiotics to combat brain-related dysfunction offer a promising approach, provided future research elucidates their mode of action and possible side effects. Further studies are warranted to establish how pre- and probiotic interventions may help to balance brain function in healthy and diseased individuals.

Urolithin Metabotypes can Anticipate the Different Restoration of the Gut Microbiota and Anthropometric Profiles during the First Year Postpartum

The metabolism of dietary polyphenols ellagitannins by the gut-microbiota allows the human stratification in urolithin metabotypes depending on the final urolithins produced. Metabotype-A only produces urolithin-A, metabotype-B yields urolithin-B and isourolithin-A in addition to urolithin-A, and metabotype 0 does not produce urolithins. Metabotype-A has been suggested to be ‘protective’, and metabotype-B dysbiotic-prone to cardiometabolic impairments. We analyzed the gut-microbiome of 40 healthy women and determined their metabotypes and enterotypes, and their associations with anthropometric and gut-microbial changes after 3 weeks, 4, 6, and 12 months postpartum. Metabotype-A was predominant in mothers who lost weight (≥2 kg) (75%) versus metabotype-B (54%). After delivery, the microbiota of metabotype-A mothers changed, unlike metabotype-B, which barely changed over 1 year. The metabotype-A discriminating bacteria correlated to the decrease of the women’s waist while some metabotype-B bacteria were inversely associated with a reduction of body mass index (BMI), waist, and waist-to-hip ratio. Metabotype-B was associated with a more robust and less modulating microbial and anthropometric profiles versus metabotype-A, in which these profiles were normalized through the 1-year follow-up postpartum. Consequently, urolithin metabotypes assessment could be a tool to anticipate the predisposition of women to normalize their anthropometric values and gut-microbiota, significantly altered during pregnancy and after childbirth.

Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal

BACKGROUND

Gut parasites exert an important influence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic inflammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species.

AIMS

We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans.

METHODS

Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis, Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for differences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples.

RESULTS

For Blastocystis, twelve differentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus-Methanobrevibacter enterotype markers, replicate findings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis, unlike Strongyloides, is associated to a "poor health" gut microbiome, as does the fact that Faecalibacterium, a bacterium with gut protective traits, is absent in Blastocystis-positive samples. Strongyloides was associated to Alloprevotella and five other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite-specific niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disentangle biological from artefactual associations between gut microbiomes and parasites.

A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease

Increasing evidence indicates that dysbiosis in the gut microbiota contributes to disease pathogenesis. However, whether certain taxa are universally indicative of diverse shrimp diseases is unclear thus far. We conducted a meta-analysis to explore the divergences in gut microbiota between healthy and diseased shrimp. The gut bacterial communities of healthy shrimp varied significantly (P < 0.05 in each comparison) over ontogenetic stages, and were distinct from the corresponding diseased cohorts at each life stage. Both phylogenetic-based mean nearest taxon distance analysis and multivariate dispersion testing revealed that shrimp disease weakened the relative importance of deterministic processes in governing the gut microbiota. Partitioning beta diversity analysis indicated that temporal turnover governed the gut microbiota as healthy shrimp aged, whereas this trend was retarded in disease cohorts, concurrent with an increased nestedness. After ruling out the age-discriminatory and disease-specific orders, a high diagnosed accuracy (85.9%) of shrimp health status was achieved by using the profiles of the 11 universal disease-discriminatory orders as independent variables. These findings improve current understanding of how disease alters the ecological processes that govern the shrimp gut microbiota assembly, and exemplifies the potential application of universal bacterial signatures to diagnose the incidence of diverse shrimp diseases, irrespective of causal pathogens.

Supplementation of triple viable probiotics combined with dietary intervention is associated with gut microbial improvement in humans on a high-fat diet

Numerous animal studies have demonstrated that oral probiotics may have a beneficial role in preventing obesity, inflammatory bowel disease and even colorectal cancer, which are all associated with a high-fat diet (HFD). However, the underlying beneficial effects of combined probiotic and dietary intervention on the gut microbiota of 'non-patient' individuals previously on an HFD have yet to be fully elucidated. In the present study, fecal samples were obtained from 36 volunteers on a high-fat diet and after dietary intervention for 4 months, and 16S rDNA sequencing was applied to identify how probiotics and dietary intervention had altered the composition of the microbiota. The results demonstrated that probiotics treatment and dietary intervention in combination raised the diversity of lumen microbes compared with their individual applications. A markedly separated distribution (β-diversity) was observed, confirming the difference in gut microbiota composition among the treatment groups. Bacterial taxonomic analysis demonstrated that the relative abundance of 30 species was altered among the groups following dietary intervention and/or probiotic supplementation. The majority of the species that exhibited a population increase belonged to two butyrate-producing families, Ruminococcaceae and Lachnospiraceae, whereas the species with reduced populations mainly belonged to the Bacteroidaceae family. Collectively, these results suggest that combined probiotic and dietary intervention is able to improve the gut microbiota composition of human subjects on an HFD.

Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors

Breastmilk contains a complex community of bacteria that may help seed the infant gut microbiota. The composition and determinants of milk microbiota are poorly understood. Among 393 mother-infant dyads from the CHILD cohort, we found that milk microbiota at 3-4 months postpartum was dominated by inversely correlated Proteobacteria and Firmicutes, and exhibited discrete compositional patterns. Milk microbiota composition and diversity were associated with maternal factors (BMI, parity, and mode of delivery), breastfeeding practices, and other milk components in a sex-specific manner. Causal modeling identified mode of breastfeeding as a key determinant of milk microbiota composition. Specifically, providing pumped breastmilk was consistently associated with multiple microbiota parameters including enrichment of potential pathogens and depletion of bifidobacteria. Further, these data support the retrograde inoculation hypothesis, whereby the infant oral cavity impacts the milk microbiota. Collectively, these results identify features and determinants of human milk microbiota composition, with potential implications for infant health and development.

Beyond cells - The virome in the human holobiont

Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.

Modeling the temporal dynamics of the gut microbial community in adults and infants

Given the highly dynamic and complex nature of the human gut microbial community, the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and functions of this ecosystem. One factor that could affect such time-dependent patterns is microbial interactions, wherein community composition at a given time point affects the microbial composition at a later time point. However, the field has not yet settled on the degree of this effect. Specifically, it has been recently suggested that only a minority of taxa depend on the microbial composition in earlier times. To address the issue of identifying and predicting temporal microbial patterns we developed a new model, MTV-LMM (Microbial Temporal Variability Linear Mixed Model), a linear mixed model for the prediction of microbial community temporal dynamics. MTV-LMM can identify time-dependent microbes (i.e., microbes whose abundance can be predicted based on the previous microbial composition) in longitudinal studies, which can then be used to analyze the trajectory of the microbiome over time. We evaluated the performance of MTV-LMM on real and synthetic time series datasets, and found that MTV-LMM outperforms commonly used methods for microbiome time series modeling. Particularly, we demonstrate that the effect of the microbial composition in previous time points on the abundance of taxa at later time points is underestimated by a factor of at least 10 when applying previous approaches. Using MTV-LMM, we demonstrate that a considerable portion of the human gut microbiome, both in infants and adults, has a significant time-dependent component that can be predicted based on microbiome composition in earlier time points. This suggests that microbiome composition at a given time point is a major factor in defining future microbiome composition and that this phenomenon is considerably more common than previously reported for the human gut microbiome.

The ability to characterize and predict temporal trajectories of the microbial community in the human gut is crucial to our understanding of the structure and functions of this ecosystem. In this study we develop MTV-LMM, a method for modeling time-series microbial community data. Using MTV-LMM we find that in contrast to previous reports, a considerable portion of microbial taxa in both infants and adults display temporal structure that is predictable using the previous composition of the microbial community. In reaching this conclusion we have adopted a number of concepts common in statistical genetics for use with longitudinal microbiome studies. We introduce concepts such as time-explainability and the temporal kinship matrix, which we believe will be of use to other researchers studying microbial dynamics, through the framework of linear mixed models. In particular we find that the association matrix estimated by MTV-LMM reveals known phylogenetic relationships and that the temporal kinship matrix uncovers known temporal structure in infant microbiome and inter-individual differences in adult microbiome. Finally, we demonstrate that MTV-LMM significantly outperforms commonly used methods for temporal modeling of the microbiome, both in terms of its prediction accuracy as well as in its ability to identify time-dependent taxa.

Optimal Microbiome Networks: Macroecology and Criticality

The human microbiome is an extremely complex ecosystem considering the number of bacterial species, their interactions, and its variability over space and time. Here, we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model, we detected potential species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detected an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and how these should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest Pareto total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not necessarily at the phase transition between healthy and unhealthy states. We stress the importance of considering portfolios of interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their interactions (i.e., species collective behavior) that shape transition from healthy to unhealthy states. The macroecological characterization of the microbiome is useful for public health and disease diagnosis and etiognosis, while species-specific analyses can detect beneficial species leading to personalized design of pre- and probiotic treatments and microbiome engineering.

Impact of Gut Microbiota Composition on Onset and Progression of Chronic Non-Communicable Diseases

In recent years, mounting scientific evidence has emerged regarding the evaluation of the putative correlation between the gut microbiota composition and the presence of chronic non-communicable diseases (NCDs), such as diabetes mellitus, chronic kidney disease, and arterial hypertension. The aim of this narrative review is to examine the current literature with respect to the relationship between intestinal dysbiosis and the insurgence/progression of chronic NCDs, analyzing the physiopathological mechanisms that can induce microbiota modification in the course of these pathologies, and the possible effect induced by microbiota alteration upon disease onset. Therapy based on probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplant can represent a useful therapeutic tool, as has been highlighted on animal studies. To this moment, clinical studies that intended to demonstrate the beneficial effect induced by this kind of oral supplementation on the gut microbiota composition, and subsequent amelioration of signs and symptoms of chronic NCDs have been conducted on limited sample populations for a limited follow-up period. Therefore, to fully evaluate the therapeutic value of this kind of intervention, it would be ideal to design ample population; randomized clinical trials with a lengthy follow up period.

Current understanding of the human microbiome

Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.

Disruption of sleep architecture in Prevotella enterotype of patients with obstructive sleep apnea-hypopnea syndrome

INTRODUCTION

Intermittent hypoxia and sleep fragmentation are critical pathophysiological processes involved in obstructive sleep apnea-hypopnea syndrome (OSAHS). Those manifestations independently affect similar brain regions and contribute to OSAHS-related comorbidities that are known to be related to the host gut alteration microbiota. We hypothesized that gut microbiota disruption may cross talk the brain function via the microbiota-gut-brain axis. Thus, we aim to survey enterotypes and polysomnographic data of patients with OSAHS.

METHODS

Subjects were diagnosed by polysomnography, from whom fecal samples were obtained and analyzed for the microbiome composition by variable regions 3-4 of 16S rRNA pyrosequencing and bioinformatic analyses. We examined the fasting levels of interleukin-6 and tumor necrosis factor-alpha of all subjects.

RESULTS

Three enterotypes Bacteroides, Ruminococcus, and Prevotella were identified in patients with OSAHS. Arousal-related parameters or sleep stages are significantly disrupted in apnea-hypopnea index (AHI) ≥15 patients with Prevotella enterotype; further analysis this enterotype subjects, obstructive, central, and mixed apnea indices, and mean heart rate are also significantly elevated in AHI ≥15 patients. However, blood cytokines levels of all subjects were not significantly different.

CONCLUSIONS

This study indicates the possibility of pathophysiological interplay between enterotypes and sleeps structure disruption in sleep apnea through a microbiota-gut-brain axis and offers some new insight toward the pathogenesis of OSAHS.

The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women

Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.

Xenobiotics Formed during Food Processing: Their Relation with the Intestinal Microbiota and Colorectal Cancer

The colonic epithelium is exposed to a mixture of compounds through diet, among which some are procarcinogens, whereas others have a protective effect. Therefore, the net impact of these compounds on human health depends on the overall balance between all factors involved. Strong scientific evidence has demonstrated the relationship between nitrosamines (NA), heterocyclic amines (HCAs), and polycyclic aromatic hydrocarbons (PAHs), which are the major genotoxins derived from cooking and food processing, and cancer. The mechanisms of the relationship between dietary toxic xenobiotics and cancer risk are not yet well understood, but it has been suggested that differences in dietary habits affect the colonic environment by increasing or decreasing the exposure to mutagens directly and indirectly through changes in the composition and activity of the gut microbiota. Several changes in the proportions of specific microbial groups have been proposed as risk factors for the development of neoplastic lesions and the enrichment of enterotoxigenic microbial strains in stool. In addition, changes in the gut microbiota composition and activity promoted by diet may modify the faecal genotoxicity/cytotoxicity, which can be associated with a higher or lower risk of developing cancer. Therefore, the interaction between dietary components and intestinal bacteria may be a modifiable factor for the development of colorectal cancer in humans and deserves more attention in the near future.

Stereotypes About Enterotype: the Old and New Ideas

In 2011, the term “enterotype” first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view. We firstly illustrated the definition of the enterotype and various factors influencing enterotypes, such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis. Finally, we showed that the concept of enterotype has been extended to other ecological niches. Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.

The human microbiome in health and disease: hype or hope

OBJECTIVES

The prognostic, diagnostic, and therapeutic potential of the human gut microbiota is widely recognised. However, translation of microbiome findings to clinical practice is challenging. Here, we discuss current knowledge and applications in the field.

METHODS

We revisit some recent advances in the field of faecal microbiome analyses with a focus on covariate analyses and ecological interpretation.

RESULTS

Population-level characterization of gut microbiota variation among healthy volunteers has allowed identifying microbiome covariates required for clinical studies. Currently, microbiome research is moving from relative to quantitative approaches that will shed a new light on microbiota-host interactions in health and disease.

CONCLUSIONS

Covariate characterization and technical advances increase reproducibility of microbiome research. Targeted in vitro/in vivo intervention studies will accelerate clinical implementation of microbiota findings.

Sex Differences in Gut Microbiota

Humans carry numerous symbiotic microorganisms in their body, most of which are present in the gut. Although recent technological advances have produced extensive research data on gut microbiota, there are various confounding factors (e.g., diet, race, medications) to consider. Sex is one of the important variables affecting the gut microbiota, but the association has not yet been sufficiently investigated. Although the results are inconsistent, several animal and human studies have shown sex differences in gut microbiota. Herein, we review these studies to discuss the sex-dependent differences as well as the possible mechanisms involved.

Microbiome as a therapeutic target in alcohol-related liver disease

Alcohol-related liver disease is associated with significant changes in gut microbial composition. The transmissibility of ethanol-induced liver disease has been demonstrated using faecal microbiota transfer in preclinical models. This technique has also led to improved survival in patients with severe alcoholic hepatitis, suggesting that changes in the composition and function of the gut microbiota are causatively linked to alcohol-related liver disease. A major mechanism by which gut microbiota influence the development of alcohol-related liver disease is through a leaky intestinal barrier. This permits translocation of viable bacteria and microbial products to the liver, where they induce and promote inflammation, as well as contribute to hepatocyte death and the fibrotic response. In addition, gut dysbiosis is associated with changes in the metabolic function of the intestinal microbiota, bile acid composition and circulation, immune dysregulation during onset and progression of alcohol-related liver disease. Findings from preclinical and human studies will be used to demonstrate how alcohol causes intestinal pathology and contributes to alcohol-related liver disease and how the latter is self-perpetuating. Additionally, we summarise the effects of untargeted treatment approaches on the gut microbiota, such as diet, probiotics, antibiotics and faecal microbial transplantation in alcohol-related liver disease. We further discuss how targeted approaches can restore intestinal homeostasis and improve alcohol-related liver disease. These approaches are likely to add to the therapeutic options for alcohol-related liver disease independently or in conjunction with steroids.

An insight into gut microbiota and its functionalities

Gut microbiota has evolved along with their hosts and is an integral part of the human body. Microbiota acquired at birth develops in parallel as the host develops and maintains its temporal stability and diversity through adulthood until death. Recent developments in genome sequencing technologies, bioinformatics and culturomics have enabled researchers to explore the microbiota and in particular their functions at more detailed level than before. The accumulated evidences suggest that though a part of the microbiota is conserved, the dynamic members vary along the gastrointestinal tract, from infants to elderly, primitive tribes to modern societies and in different health conditions. Though the gut microbiota is dynamic, it performs some basic functions in the immunological, metabolic, structural and neurological landscapes of the human body. Gut microbiota also exerts significant influence on both physical and mental health of an individual. An in-depth understanding of the functioning of gut microbiota has led to some very exciting developments in therapeutics, such as prebiotics, probiotics, drugs and faecal transplantation leading to improved health.

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome's link to Pseudocapillaria tomentosa infection and pathology

BACKGROUND

Helminth parasites represent a significant threat to the health of human and animal populations, and there is a growing need for tools to treat, diagnose, and prevent these infections. Recent work has turned to the gut microbiome as a utilitarian agent in this regard; components of the microbiome may interact with parasites to influence their success in the gut, meaning that the microbiome may encode new anthelmintic drugs. Moreover, parasite infections may restructure the microbiome's composition in consistent ways, implying that the microbiome may be useful for diagnosing infection. The innovation of these utilities requires foundational knowledge about how parasitic infection, as well as its ultimate success in the gut and impact on the host, relates to the gut microbiome. In particular, we currently possess limited insight into how the microbiome, host pathology, and parasite burden covary during infection. Identifying interactions between these parameters may uncover novel putative methods of disrupting parasite success.

RESULTS

To identify interactions between parasite success and the microbiome, we quantified longitudinal associations between an intestinal helminth of zebrafish, Pseudocapillaria tomentosa, and the gut microbiome in 210 4-month-old 5D line zebrafish. Parasite burden and parasite-associated pathology varied in severity throughout the experiment in parasite-exposed fish, with intestinal pathologic changes becoming severe at late time points. Parasite exposure, burden, and intestinal lesions were correlated with gut microbial diversity. Robust generalized linear regression identified several individual taxa whose abundance predicted parasite burden, suggesting that gut microbiota may influence P. tomentosa success. Numerous associations between taxon abundance, burden, and gut pathologic changes were also observed, indicating that the magnitude of microbiome disruption during infection varies with infection severity. Finally, a random forest classifier accurately predicted a fish's exposure to the parasite based on the abundance of gut phylotypes, which underscores the potential for using the gut microbiome to diagnose intestinal parasite infection.

CONCLUSIONS

These experiments demonstrate that P. tomentosa infection disrupts zebrafish gut microbiome composition and identifies potential interactions between the gut microbiota and parasite success. The microbiome may also provide a diagnostic that would enable non-destructive passive sampling for P. tomentosa and other intestinal pathogens in zebrafish facilities.

Intestinal parasitic infection alters bacterial gut microbiota in children

The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children's care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.

Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children

BACKGROUND

The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children.

RESULTS

Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus.

CONCLUSIONS

Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.

Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition

BACKGROUND

The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.

RESULTS

Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations.

CONCLUSIONS

We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.

Clinician Guide to Microbiome Testing

Recent recognition that the intestinal microbiome plays potential roles in the pathogenesis of multiple common diseases has led to a growing interest in personalized microbiome analysis among clinical investigators and patients. Permissibility of direct access testing has allowed the emergence of commercial companies offering microbiome analysis to patients seeking to gain a better understanding of their symptoms and disease conditions. In turn, physicians are often asked to help with interpretation of such tests or even requested by their patients to order them. Therefore, physicians need to have a basic understanding of the current state of microbiome science. This review examines how the perspective of microbial ecology, which is fundamental to understanding the microbiome, updates the classical version of the germ theory of disease. We provide the essential vocabulary of microbiome science and describe its current limitations. We look forward to the future when microbiome diagnostics may live up to its potential of becoming integral to clinical care that will become increasingly individualized, and microbiome analysis may become incorporated into that future paradigm. However, we caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.

Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome

The poultry industry has traditionally relied on the use of antibiotic growth promoters (AGPs) to improve production efficiency and minimize infection. With the recent drive to eliminate the use of AGPs, novel alternatives are urgently required. Recently attention has turned to the use of synthetic communities that may be used to ‘seed’ the developing microbiome. The current challenge is identifying keystone taxa whose influences in the gut can be leveraged for probiotic development. To help define such taxa we present a meta-analysis of 16S rRNA surveys of 1572 cecal microbiomes generated from 19 studies. Accounting for experimental biases, consistent with previous studies, we find that AGP exposure can result in reduced microbiome diversity. Network community analysis defines groups of taxa that form stable clusters and further reveals Lactobacillus to elicit a polarizing effect on the cecal microbiome, exhibiting relatively equal numbers of positive and negative interactions with other taxa. Our identification of stable taxonomic associations provides a valuable framework for developing effective microbial consortia as alternatives to AGPs.

Resveratrol, Metabolic Syndrome, and Gut Microbiota

Resveratrol is a polyphenol which has been shown to have beneficial effects on metabolic syndrome-related alterations in experimental animals, including glucose and lipid homeostasis improvement and a reduction in fat mass, blood pressure, low-grade inflammation, and oxidative stress. Clinical trials have been carried out to address its potential; however, results are still inconclusive. Even though resveratrol is partly metabolized by gut microbiota, the relevance of this “forgotten organ” had not been widely considered. However, in the past few years, data has emerged suggesting that the therapeutic potential of this compound may be due to its interaction with gut microbiota, reporting changes in bacterial composition associated with beneficial metabolic outcomes. Even though data is still scarce and for the most part observational, it is promising nevertheless, suggesting that resveratrol supplementation could be a useful tool for the treatment of metabolic syndrome and its associated conditions.

Neonatal gut and respiratory microbiota: coordinated development through time and space

BACKGROUND

Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions and functions. Associations between microbiota at multiple sites represent an unexplored influence on the infant microbiome. Here, we examined co-occurrence patterns of gut and respiratory microbiota in pre- and full-term infants over the first year of life, a period critical to neonatal development.

RESULTS

Gut and respiratory microbiota collected as longitudinal rectal, throat, and nasal samples from 38 pre-term and 44 full-term infants were first clustered into community state types (CSTs) on the basis of their compositional profiles. Multiple methods were used to relate the occurrence of CSTs to temporal microbiota development and measures of infant maturity, including gestational age (GA) at birth, week of life (WOL), and post-menstrual age (PMA). Manifestation of CSTs followed one of three patterns with respect to infant maturity: (1) chronological, with CST occurrence frequency solely a function of post-natal age (WOL), (2) idiosyncratic to maturity at birth, with the interval of CST occurrence dependent on infant post-natal age but the frequency of occurrence dependent on GA at birth, and (3) convergent, in which CSTs appear first in infants of greater maturity at birth, with occurrence frequency in pre-terms converging after a post-natal interval proportional to pre-maturity. The composition of CSTs was highly dissimilar between different body sites, but the CST of any one body site was highly predictive of the CSTs at other body sites. There were significant associations between the abundance of individual taxa at each body site and the CSTs of the other body sites, which persisted after stringent control for the non-linear effects of infant maturity. Canonical correlations exist between the microbiota composition at each pair of body sites, with the strongest correlations between proximal locations.

CONCLUSION

These findings suggest that early microbiota is shaped by neonatal innate and adaptive developmental responses. Temporal progression of CST occurrence is influenced by infant maturity at birth and post-natal age. Significant associations of microbiota across body sites reveal distal connections and coordinated development of the infant microbial ecosystem.

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.

The bacteriome at the onset of type 1 diabetes: A study from four geographically distant African and Asian countries

OBJECTIVES

Gut bacteriome profiling studies in type 1 diabetes (T1D) to date are mostly limited to populations of Europe, with two studies from China and one study each from Mexico and the USA. We therefore sought to characterize the stool bacteriome in children after onset of T1D along with age- and place-matched control subjects from four geographically distant African and Asian countries.

METHODS

Samples were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 104 matched control subjects of similar age and locale. Genotyping of major T1D susceptibility genes was performed using saliva or blood samples. The bacteriome was profiled by next-generation sequencing of 16S rDNA. Negative binomial regression was used to model associations, with adjustment for the matched structure of the study.

RESULTS

A significant positive association with T1D was noted for the genus Escherichia (class Gammaproteobacteria, phylum Proteobacteria), whereas Eubacterium and Roseburia, two genera of class Clostridia, phylum Firmicutes, were inversely associated with T1D. We also confirmed a previously observed inverse association with Clostridium clusters IV or XIVa. No associations were noted for richness, evenness, or enterotypes.

CONCLUSIONS

Based on our results, some type of distortion of the gut bacteriome appears to be a global feature of T1D, and our findings for four distant populations add new candidates to the existing list of bacteria. It remains to be established whether the observed associations are markers or causative factors.

Dietary Interventions to Modulate the Gut Microbiome-How Far Away Are We From Precision Medicine

The importance of the gut microbiome in human health and disease is fully acknowledged. A perturbation in the equilibrium among the different microbial populations living in the gut (dysbiosis) has been associated with the development of several types of diseases. Modulation of the gut microbiome through dietary intervention is an emerging therapeutic and preventive strategy for many conditions. Nevertheless, interpersonal differences in response to therapeutic treatments or dietary regimens are often observed during clinical trials, and recent research has suggested that subject-specific features of the gut microbiota may be responsible. In this review, we summarize recent findings in personalized nutrition, highlighting how individualized characterization of the microbiome may assist in designing ad hoc tailored dietary intervention for disease treatment and prevention. Moreover, we discuss the limitations and challenges encountered in integrating patient-specific microbial data into clinical practice.

GePMI: A statistical model for personal intestinal microbiome identification

Human gut microbiomes consist of a large number of microbial genomes, which vary by diet and health conditions and from individual to individual. In the present work, we asked whether such variation or similarity could be measured and, if so, whether the results could be used for personal microbiome identification (PMI). To address this question, we herein propose a method to estimate the significance of similarity among human gut metagenomic samples based on reference-free, long k-mer features. Using these features, we find that pairwise similarities between the metagenomes of any two individuals obey a beta distribution and that a p value derived accordingly well characterizes whether two samples are from the same individual or not. We develop a computational framework called GePMI (Generating inter-individual similarity distribution for Personal Microbiome Identification) and apply it to several human gut metagenomic datasets (>300 individuals and >600 samples in total). From the results of GePMI, most of the human gut microbiomes can be identified (auROC = 0.9470, auPRC = 0.8702). Even after antibiotic treatment or fecal microbiota transplantation, the individual k-mer signature still maintains a certain specificity.

Physiology and central carbon metabolism of the gut bacterium Prevotella copri

The human gut microbiota is a crucial factor for the host's physiology with respect to health and disease. Metagenomic shotgun sequencing of microbial gut communities revealed that Prevotella copri is one of the most important players in the gastrointestinal tract of many individuals. Because of the importance of this bacterium we analyzed the growth behavior and the central metabolic pathways of P. copri. Bioinformatic data, transcriptome profiling and enzyme activity measurements indicated that the major pathways are based on glycolysis and succinate production from fumarate. In addition, pyruvate can be degraded to acetate and formate. Electron transport phosphorylation depends on fumarate respiration with NADH and reduced ferredoxin as electron donors. In contrast to Bacteroides vulgatus, P. copri showed a more pronounced dependency on the addition of CO₂ or bicarbonate for biomass formation, which is a remarkable difference between P. copri and Bacteroides spp. with important implication in the context of gut microbial competition. The analysis of substrate consumption and product concentrations from many P. copri cultures with different optical densities allowed a prediction of the carbon and electron flow in the central metabolism and a detailed calculation of growth yields as well as carbon and redox balances.

Lawsonia intracellularis: Revisiting the Disease Ecology and Control of This Fastidious Pathogen in Pigs

Lawsonia intracellularis is an anaerobic obligate intracellular bacterium infecting the small intestine and infrequently also the large intestine of pigs and other animals including hamsters and horses. The infection is characterized by proliferation, hemorrhage, necrosis, or any combination commonly referred to as "ileitis," affecting the health and production efficacy of farmed pigs. Despite decades of research on this pathogen, the pathogenesis and virulence factors of this organism are not clearly known. In pigs, prophylaxis against L. intracellularis infection is achieved by either administration of subtherapeutic levels of in-feed antibiotic growth promoters or vaccination. While the former approach is considered to be effective in L. intracellularis control, potential regulations on subtherapeutic antibiotics in many countries in the near future may necessitate alternative approaches. The potential of manipulating the gut microbiome of pigs with feed ingredients or supplements to control L. intracellularis disease burden is promising based on the current understanding of the porcine gut microbiome in general, as well as preliminary insights into the disease ecology of L. intracellularis infection accrued over the last 30 years.

CLOUD: a non-parametric detection test for microbiome outliers

BACKGROUND

Dysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set of metabolic, auto-immune, and infectious diseases, and yet there is substantial inter-individual variation in microbiome composition even within body sites of healthy humans. An individual's microbiome varies over time in a high-dimensional space to form their personal microbiome cloud. This cloud may or may not be similar to that of other people, both in terms of the average microbiome profile (conformity) and the diameter of the cloud (stability). However, there is currently no robust non-parametric test that determines whether a patient's microbiome cloud is an outlier with respect to a reference group of healthy individuals with widely varying microbiome profiles.

METHODS

Here, we propose a test for outliers' detection in the human gut microbiome that accounts for the wide range of microbiome phenotypes observed in a typical set of healthy individuals and for intra-individual temporal variation. Our robust nonparametric outlier detection test, the CLOUD test, performs two assessments of a patient's microbiome health: conformity, the extent to which the patient's microbiome cloud is ecologically similar to a subset of healthy subjects; and stability, which compares the cloud diameter of a patient to those of healthy subjects. The CLOUD test is based on locally linear embedded ecological distances, allowing it to account for widely varying microbiome compositions among reference individuals. It also leverages temporal variability within patients and reference individuals to increase the robustness of the test.

RESULTS

We describe the CLOUD test, and we apply it to one novel and two previously published cohorts of patients receiving fecal microbiota transplantation for recurrent Clostridium difficile colitis, as well as to two known healthy cohorts, demonstrating high concordance of the CLOUD conformity and stability indices with clinical outcomes.

CONCLUSIONS

Although the CLOUD test is not, on its own, a test for clinical dysbiosis, it nonetheless provides a framework for outlier testing that could be incorporated into evaluation of suspected dysbiosis, which may play a role in diagnosis and prognosis of numerous pediatric and adult diseases.

Microbial communities as dynamical systems

Nowadays, microbial communities are frequently monitored over long periods of time and the interactions between their members are explored in vitro. This development has opened the way to apply mathematical models to characterize community structure and dynamics, to predict responses to perturbations and to explore general dynamical properties such as stability, alternative stable states and periodicity. Here, we highlight the role of dynamical systems theory in the exploration of microbial communities, with a special emphasis on the generalized Lotka-Volterra (gLV) equations. In particular, we discuss applications, assumptions and limitations of the gLV model, mention modifications to address these limitations and review stochastic extensions. The development of dynamical models, together with the generation of time series data, can improve the design and control of microbial communities.

Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence

It is now recognized that gut microbiota contributes indispensable roles in safeguarding host health. Shrimp is being threatened by newly emerging diseases globally; thus, understanding the driving factors that govern its gut microbiota would facilitate an initial step to reestablish and maintain a "healthy" gut microbiota. This review summarizes the factors that assemble the shrimp gut microbiota, which focuses on the current progresses of knowledge linking the gut microbiota and shrimp health status. In particular, I propose the exploration of shrimp disease pathogenesis and incidence based on the interplay between dysbiosis in the gut microbiota and disease severity. An updated research on shrimp disease toward an ecological perspective is discussed, including host-bacterial colonization, identification of polymicrobial pathogens and diagnosing disease incidence. Further, a simple conceptual model is offered to summarize the interplay among the gut microbiota, external factors, and shrimp disease. Finally, based on the review, current limitations are raised and future studies directed at solving these concerns are proposed. This review is timely given the increased interest in the role of gut microbiota in disease pathogenesis and the advent of novel diagnosis strategies.