Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants

Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.

Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases

Gut microbiota represents a complex physiological ecosystem that influences the host health. Alterations in the microbiome metabolism affect the body homeostasis and they have been associated with the development of different human neurodegenerative and neuropsychiatric disorders, such as Alzheimer's disease, autism spectrum disorder, bipolar disorder, depression, Huntington's disease, Parkinson's disease, posttraumatic stress disorder and schizophrenia. The development of these complex diseases is influenced by various factors, including genetic predisposition and environmental triggers. Gut microbiota has recently emerged as an important actor in their physiopathology that has been shown to play a role in inflammation, oxidative stress, and gut permeability. Therefore, targeting the metabolites that are produced by or associated with the gut microbiota may help us understand how imbalance in the gut-brain axis affects human health. This review offers a comprehensive overview of the literature on this matter, offering the readers an insight in the state-of-art metabolic measurements of the gut-brain axis in various brain-related diseases.

From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

Microbiome: Evolution in a World of Interaction

Ecological interactions can generate strong selection. Two new studies reveal that the tempo and patterns of evolutionary change in a mammalian gut commensal can be altered dramatically during interactions with both the host and its microbiome.

Impact of the Human Microbiome in Forensic Sciences: a Systematic Review

Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible contributions to the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out by following PRISMA guidelines. This study sheds light on the role of microbiome research in the postmortem interval during the process of decomposition, identifying death caused by drowning or sudden death, locating the geographical location of death, establishing a connection between the human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae, and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori can be used to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes

The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Microbiota and Lung Cancer. Opportunities and Challenges for Improving Immunotherapy Efficacy

The advances in molecular biology and the emergence of Next Generation Sequencing (NGS) have revealed that microbiome composition is closely related with health and disease, including cancer. This relationship affects different levels of cancer such as development, progression, and response to treatment including immunotherapy. The efficacy of immune checkpoint inhibitors (ICIs) may be influenced by the concomitant use of antibiotics before, during or shortly after treatment with ICIs. Nevertheless, the linking mechanism between microbiote, host immunity and cancer is not clear and the role of microbiota manipulation and analyses in cancer management has not been clinically validated yet. Regarding the use of microbiome as biomarker to predict ICI efficacy it has been recently shown that the use of biochemical serum markers to monitor intestinal permeability and loss of barrier integrity, like citrulline, could be useful to monitor microbiota changes and predict ICI efficacy. There are still many unknowns about the role of these components, their relationship with the microbiota, with the use of antibiotics and the response to immunotherapy. The next challenge in microbiome research will be to identify individual microbial species that causally affect lung cancer phenotypes and response to ICI and disentangle the underlying mechanisms. Thus, further analyses in patients with lung cancer receiving treatment with ICIs and its correlation with the composition of the microbiota in different organs including the respiratory tract, peripheral blood and intestinal tract could be useful to predict the efficacy of ICIs and its modulation with antibiotic use.

Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections

AIM

To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.

METHODOLOGY

Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.

RESULTS

Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P < 0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.

CONCLUSION

The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.

Fermentation of prebiotics by human colonic microbiota in vitro and short-chain fatty acids production: a critical review

Prebiotics are known for their health benefits to man, including reducing cardiovascular disease and improving gut health. This review takes a critical assessment of the impact of dietary fibres and prebiotics on the gastrointestinal microbiota in vitro. The roles of colonic organisms, slow fermentation of prebiotics, production of high butyric and propionic acids and positive modulation of the host health were taken into cognizance. Also, the short-chain fatty acids (SCFAs) molecular signalling mechanisms associated with their prebiotic substrate structural conformations and the phenotypic responses related to the gut microbes composition were discussed. Furthermore, common dietary fibres such as resistant starch, pectin, hemicelluloses, β-glucan and fructan in context of their prebiotic potentials for human health were also explained. Finally, the in vitro human colonic fermentation depends on prebiotic type and its physicochemical characteristics, which will then affect the rate of fermentation, selectivity of micro-organisms to multiply, and SCFAs concentrations and compositions.

Artificial Larval Diet Mediates the Microbiome of Queensland Fruit Fly

Larval diets used for artificial rearing can have a significant effect on insect biology. The Queensland fruit fly (aka "Qfly"), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is one of the greatest challenges for fruit growers in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to reduce populations in regions where this species is endemic. Factory scale rearing is essential for SIT; however, artificial larval diets are known to affect the microbiome of Qfly, which may then affect fly performance. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared, for five generations from nature, on two common artificial diets (carrot and gel). At generation five (G5), the microbiome was assessed in larvae, pupae, adult males and adult females and standard fly quality control parameters were assessed together with additional performance measures of mating propensity and survival under nutritional stress. At the genus level, bacterial communities were significantly different between the colonies reared on the two larval diets. However, communities converged at Phyla to family taxonomic levels. Bacterial genera of Morganella, Citrobacter, Providencia, and Burkholderia were highly abundant in all developmental stages of Qfly reared on the gel diet, when compared to the carrot diet. Despite abundance of these genera, a greater percentage of egg hatching, heavier pupal weight and a higher percentage of fliers were found in the Qfly reared on the gel diet. Mating propensity and survival under nutritional stress was similar for adult Qfly that had been reared on the two larval diets. Overall, our findings demonstrate that the artificial larval diet strongly influences the microbiome and quality control measures of Qfly, with likely downstream effects on performance of flies released in SIT programs.

Islamic fasting leads to an increased abundance of Akkermansia muciniphila and Bacteroides fragilis group: A preliminary study on intermittent fasting

BACKGROUND/AIMS

It has been largely accepted that dietary habits affect intestinal microbiota composition. In this pilot study, we hypothesized that time-restricted feeding, which can be regarded as a type of intermittent fasting, may have a distinct effect on intestinal microbiota. Ramadan fasting is an excellent model to understand how time-restricted feeding affect the microbiota.

MATERIALS AND METHODS

A total of nine subjects were included in this study during Ramadan, consisting of 17 h of fasting/day during a 29-day period. Stool samples were collected at baseline and the day of the end of Ramadan. 16S rRNA qPCR assay has been performed for quantification of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium spp., Lactobacillus spp., Bacteroides fragilis group, and Enterobacteriaceae. Blood samples were also collected to test for metabolic and nutritional parameters.

RESULTS

A significantly increased abundance of A. muciniphila and B. fragilis group was observed in all subjects after Islamic fasting when compared with the baseline levels (p=0.004 and 0.008, respectively). Serum fasting glucose and total cholesterol levels were also significantly reduced in all of the subjects (p<0.01 and p=0.009, respectively).

CONCLUSION

Islamic fasting, which represents intermittent fasting, leads to an increase in A. muciniphila and B. fragilis group, which were considered as healthy gut microbiota members. Although this is a pilot study, which should be tested with larger sample size, there are a very limited number of studies in the literature on fasting and microbiota in human subjects. Thus, our present findings may contribute to the understanding of fasting-gut microbiota interaction.

Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface

Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.

Comparison of Gut Microbiota Diversity and Predicted Functions Between Healthy and Diseased Captive Rana dybowskii

The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota assembly remains unclear and gut microbiota-based predictions of health status is a promising yet poorly established field. Using Illumina high-throughput sequencing technology, we compared the gut microbiota between healthy (HA and HB) and diarrhoeic (DS) Rana dybowskii groups and analyzed the functional profiles through a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. In addition, we estimated the correlation between gut microbiota structures and predicted the functional compositions. The results showed significant differences in the phylogenetic diversity (Pd), Shannon, and observed richness (Sobs) indices between the DS and HB groups, with significant differences observed in the gut microbiota composition between the DS group and the HA and HB groups. Linear discriminant analysis (LDA) effect size (LEfSe) results revealed that Proteobacteria were significantly enriched in the DS group; Bacteroidetes were significantly enriched in the HA and HB groups; and Aeromonas, Citrobacter, Enterococcus, Hafnia-Obesumbacterium, Morganella, Lactococcus, Providencia, Vagococcus, and Staphylococcus were significantly enriched in the DS group. Venn diagrams revealed that there were many more unique genera in the DS group than the HA and HB groups. Among 102 sensitive species selected using the indicator method, 33 indicated a healthy status and 69 (e.g., Acinetobacter, Aeromonas, Legionella, Morganella, Proteus, Providencia, Staphylococcus, and Vagococcus) indicated a diseased status. There was a significant and positive association between the composition and functional composition of the gut microbiota, thus indicating low functional redundancy of the frog gut bacterial community. Rana dybowskii disease was associated with changes in the gut microbiota, which subsequently disrupted bacterial-mediated functions. The results of this study can aid in revealing the effect of the R. dybowskii gut microbiota on host health and provide a basis for elucidating the mechanism of the occurrence of R. dybowskii disease.

Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls, and Challenges

Over the last 15 years, the advent of high-throughput "omics" techniques has revealed the multiple roles and interactions occurring among hosts, their microbial partners and their environment. This microbiome revolution has radically changed our views of biology, evolution, and individuality. Sitting at the interface between a host and its environment, the microbiome is a relevant yet understudied compartment for ecotoxicology research. Various recent works confirm that the microbiome reacts to and interacts with contaminants, with consequences for hosts and ecosystems. In this paper, we thus advocate for the development of a "microbiome-aware ecotoxicology" of organisms. We emphasize its relevance and discuss important conceptual and technical pitfalls associated with study design and interpretation. We identify topics such as functionality, quantification, temporality, resilience, interactions, and prediction as major challenges and promising venues for microbiome research applied to ecotoxicology.

Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change

Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.

Diversity in the Extracellular Vesicle-Derived Microbiome of Tissues According to Tumor Progression in Pancreatic Cancer

This study was conducted to identify the composition and diversity of the microbiome in tissues of pancreatic cancer and to determine its role. First, extracellular vesicles (EVs) were obtained from the paired tumor and normal tissues, and 16s rRNA gene sequencing was performed. We identified the microbiomes, compared the diversity between groups, and found that Tepidimonas was more abundant in tumors. Second, larger tumors resulted in lower levels of Leuconostoc and Sutterella, and increased lymph node metastasis resulted in higher levels of Comamonas and Turicibacter in tumor tissues. Moreover, in the case of tumor recurrence, the levels of Streptococcus and Akkermansia were decreased in tumor tissues. Finally, with the supernatant of Tepidimonasfonticaldi, proliferation and migration of cells increased, and epithelial-mesenchymal transition and the Tricarboxylic Acid (TCA) cycle-related metabolites were enhanced. The composition and diversity of EV-derived microbiomes are important for providing novel insights into theragnostic approaches in pancreatic cancer.

Immune boosting functional foods and their mechanisms: A critical evaluation of probiotics and prebiotics

Comprehensive studies conducted on the link between the gut microbiome and immunity in recent decades have correspondingly led to ever increasing interests in functional foods, especially probiotics and prebiotics. Probiotics and prebiotics play crucial roles in managing the intestinal microbiota in order to improve host health, even though their influence on other body sites are being investigated. Different colonic bacteria metabolize dietary prebiotics to produce beneficial metabolites, especially short chain fatty acids (SCFAs) that improve luminal contents and intestinal performance, while positively affecting overall host physiology. Thus, this review provides a general perspective of the immune system, the gut immune system and its microbiota. The review also evaluates functional foods with critical but comprehensive perspectives into probiotics and prebiotics, their immune boosting and mechanisms of action. It is recommended that further mechanistic and translational studies are conducted to promote health, social life and also empower poverty-stricken communities.

Optimal integration between host physiology and functions of the gut microbiome

Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities. This article is part of the theme issue 'The role of the microbiome in host evolution'.

gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics and metaproteomics in an integrative manner. The pipeline has been developed using the workflow management framework Snakemake in order to obtain an automated and reproducible pipeline. Using experimental datasets of the German cockroach Blattella germanica, a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. In conclusion, gNOMO is a bioinformatic pipeline that can easily be configured, for integrating and analyzing multiple meta-omics data types and for producing output visualizations, specifically designed for integrating paired-end sequencing data with mass spectrometry from non-model organisms.

Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study

AIMS

The gut microbiota exerts a critical influence in the immune system. The gut microbiota of human virus immunodeficiency (HIV)-infected children remains barely explored. We aimed to characterize the fecal microbiota in vertically HIV-infected children and to explore the effects of its modulation with a symbiotic nutritional intervention.

METHODS

a pilot, double blind, randomized placebo-controlled study including HIV-infected children who were randomized to receive a nutritional supplementation including prebiotics and probiotics or placebo for four weeks. HIV-uninfected siblings were recruited as controls. The V3-V4 region of the 16S rRNA gene was sequenced in fecal samples.

RESULTS

22 HIV-infected children on antiretroviral therapy (ART) and with viral load (VL) <50/mL completed the follow-up period. Mean age was 11.4 ± 3.4 years, eight (32%) were male. Their microbiota showed reduced alpha diversity compared to controls and distinct beta diversity at the genus level (Adonis p = 0.042). Patients showed decreased abundance of commensals Faecalibacterium and an increase in Prevotella, Akkermansia and Escherichia. The nutritional intervention shaped the microbiota towards the control group, without a clear directionality.

CONCLUSIONS

Vertical HIV infection is characterized by changes in gut microbiota structure, distinct at the compositional level from the findings reported in adults. A short nutritional intervention attenuated bacterial dysbiosis, without clear changes at the community level.

SUMMARY

In a group of 24 vertically HIV-infected children, in comparison to 11 uninfected controls, intestinal dysbiosis was observed despite effective ART. Although not fully effective to restore the microbiota, a short intervention with pre/probiotics attenuated bacterial dysbiosis.

The Gut Microbiome and Xenobiotics: Identifying Knowledge Gaps

There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut Microbiome: Markers of Human Health, Drug Efficacy and Xenobiotic Toxicity" (https://hesiglobal.org/event/the-gut-microbiome-workshop) to identify data gaps in determining how gut microbiome alterations may affect human health. Speakers and stakeholders from academia, government, and industry addressed multiple topics including the current science on the gut microbiome, endogenous and exogenous metabolites, biomarkers, and model systems. The workshop presentations and breakout group discussions formed the basis for identifying data gaps and research needs. Two critical issues that emerged were defining the microbial composition and function related to health and developing standards for models, methods and analysis in order to increase the ability to compare and replicate studies. A series of key recommendations were formulated to focus efforts to further understand host-microbiome interactions and the consequences of exposure to xenobiotics as well as identifying biomarkers of microbiome-associated disease and toxicity.

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats

The gut microbiota, via the production of metabolites entering the circulation, plays a role in blood pressure regulation. Blood pressure is also affected by the characteristics of sleep. To date, no studies have examined relationships among the gut microbiota/metabolites, blood pressure, and sleep. We hypothesized that fragmented sleep is associated with elevated mean arterial pressure, an altered and dysbiotic gut microbial community, and changes in fecal metabolites. In our model system, rats were randomized to 8 h of sleep fragmentation during the rest phase (light phase) or were undisturbed (controls) for 28 consecutive days. Rats underwent sleep and blood pressure recordings, and fecal samples were analyzed during: baseline (days -4 to -1), early sleep fragmentation (days 0-3), midsleep fragmentation (days 6-13), late sleep fragmentation (days 20-27), and recovery/rest (days 28-34). Less sleep per hour during the sleep fragmentation period was associated with increased mean arterial pressure. Analyses of gut microbial communities and metabolites revealed that putative short chain fatty acid-producing bacteria were differentially abundant between control and intervention animals during mid-/late sleep fragmentation and recovery. Midsleep fragmentation was also characterized by lower alpha diversity, lower Firmicutes:Bacteroidetes ratio, and higher Proteobacteria in intervention rats. Elevated putative succinate-producing bacteria and acetate-producing bacteria were associated with lower and higher mean arterial pressure, respectively, and untargeted metabolomics analysis demonstrates that certain fecal metabolites are significantly correlated with blood pressure. These data reveal associations between sleep fragmentation, mean arterial pressure, and the gut microbiome/fecal metabolome and provide insight to links between disrupted sleep and cardiovascular pathology.

Live Biotherapeutic Products, A Road Map for Safety Assessment

Recent developments in the understanding of the relationship between the microbiota and its host have provided evidence regarding the therapeutic potential of selected microorganisms to prevent or treat disease. According to Directive 2001/83/EC, in the European Union (EU), any product intended to prevent or treat disease is defined as a medicinal product and requires a marketing authorization by competent authorities prior to commercialization. Even if the pharmaceutical regulatory framework is harmonized at the EU level, obtaining marketing authorisations for medicinal products remains very challenging for Live Biotherapeutic Products (LBPs). Compared to other medicinal products currently on the market, safety assessment of LBPs represents a real challenge because of their specific characteristics and mode of action. Indeed, LBPs are not intended to reach the systemic circulation targeting distant organs, tissues, or receptors, but rather exert their effect through direct interactions with the complex native microbiota and/or the modulation of complex host-microbiota relation, indirectly leading to distant biological effects within the host. Hence, developers must rely on a thorough risk analysis, and pharmaceutical guidelines for other biological products should be taken into account in order to design relevant non-clinical and clinical development programmes. Here we aim at providing a roadmap for a risk analysis that takes into account the specificities of LBPs. We describe the different risks associated with these products and their interactions with the patient. Then, from that risk assessment, we propose solutions to design non-clinical programmes and First in Human (FIH) early clinical trials appropriate to assess LBP safety.

Rapeseed-based diet modulates the imputed functions of gut microbiome in growing-finishing pigs

Rapeseed meal is a sustainable feed ingredient that can be used as an alternative to imported soybean meal in European pig production. The gut microbiota plays an important role on pig physiology and health but the impact on microbiota of using rapeseed in diets is still not well known. In this study, 84 purebred Norwegian Landrace pigs with average initial weight of 25 kg were divided into two groups and fed for approximately three months with either a control diet containing soybean meal (CON) or a high-fiber experimental diet where 20% rapeseed meal (RSF) was included as an alternative to soybean meal in CON. The composition and function of microbiome in gut digesta samples were analyzed by performing 16S rRNA gene sequencing and culturing of bacteria. The microbiota diversity and composition were similar between the dietary treatments; however, relative abundance of a variety of bacterial groups and imputed functions of microbiome in the ileum and large intestine were altered when the pigs were fed with a rapeseed-based diet. It was notable that the immune-inducing bacterial group Mucispirillum and anti-inflammatory stimulating bacteria Lachnospira were more abundant in the ileum and large intestine of the RSF group, respectively. Moreover, there was a higher abundance of major amino acid fermenters and amylolytic bacteria in the CON group and a high abundance of putative short chain fatty acid producers in RSF group. In comparison with the CON group, the gut microbiome of RSF group possessed an enhanced potential for carbohydrate and energy metabolism and a reduced potential for bacterial pathogenicity-related pathways.

Serum and fecal profiles of aromatic microbial metabolites reflect gut microbiota disruption in critically ill patients: a prospective observational pilot study

BACKGROUND

High serum levels of certain aromatic microbial metabolites (AMM) are associated with severity and mortality in critically ill patients. Omics-based studies suggest gut dysbiosis and reduced microbiome diversity in critical conditions. However, the landscape of gut microbial metabolites is still to be outlined, not to mention the interplay correlation between the metabolome and gut microbiome in critically ill patients. The aim of this study was to analyze the association between serum and fecal levels of AMM and compare them with the composition of gut microbiota in critically ill patients in the acute and chronic stages.

METHODS

In this prospective observational pilot study, we analyzed the temporal dynamics of the gut microbiome and the AMM spectrum across two distinct subgroups-acute critical ill (ACI) patients with nosocomial pneumonia and chronically critically ill (CCI) patients (9 subjects each group)-as well as performed comparison with 23 healthy volunteers. The AMM levels for each patient were measured using GC-MS in simultaneously taken serum and fecal samples (SFS). These parameters were compared with 16S rRNA fecal microbiome profiles.

RESULTS

The observed proportions of bacterial taxa suggest a significant gut dysbiosis in the ACI and the CCI patients. Stronger imbalance in microbiome composition and dynamics observed in the ACI patients compared to the CCI ones resonates with a higher severity in the former group. The total levels of AMM in serum samples were higher for the ACI patients than for the CCI patients (3.7 (1.4-6.3) and 1.1 (1.0-1.6) μM, respectively; p = 0.0003). The qualitative composition of the SFS was also altered. We discovered significant associations between gut microbial taxa levels and metabolite concentrations in blood serum as well as in feces in each of the ACI and the CCI patients.

CONCLUSIONS

Aromatic microbial metabolite profiles in the gut and the serum are interlinked and reflect a disruption of the gut microbial community in critically ill patients.

Amoxicillin Increased Functional Pathway Genes and Beta-Lactam Resistance Genes by Pathogens Bloomed in Intestinal Microbiota Using a Simulator of the Human Intestinal Microbial Ecosystem

Antibiotics are frequently used to treat bacterial infections; however, they affect not only the target pathogen but also commensal gut bacteria. They may cause the dysbiosis of human intestinal microbiota and consequent metabolic alterations, as well as the spreading of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). In vitro experiments by simulator of the human intestinal microbial ecosystem (SHIME) can clarify the direct effects of antibiotics on different regions of the human intestinal microbiota, allowing complex human microbiota to be stably maintained in the absence of host cells. However, there are very few articles added the antibiotics into this in vitro model to observe the effects of antibiotics on the human intestinal microbiota. To date, no studies have focused on the correlations between the bloomed pathogens caused by amoxicillin (AMX) exposure and increased functional pathway genes as well as ARGs. This study investigated the influence of 600 mg day-1 AMX on human intestinal microbiota using SHIME. The impact of AMX on the composition and function of the human intestinal microbiota was revealed by 16S rRNA gene sequencing and high-throughput quantitative PCR. The results suggested that: (i) AMX treatment has tremendous influence on the overall taxonomic composition of the gut microbiota by increasing the relative abundance of Klebsiella [linear discriminant analysis (LDA) score = 5.26] and Bacteroides uniformis (LDA score = 4.75), as well as taxonomic diversity (Simpson, P = 0.067, T-test; Shannon, P = 0.061, T-test), and decreasing the members of Parabacteroides (LDA score = 4.18), Bifidobacterium (LDA score = 4.06), and Phascolarctobacterium (LDA score = 3.95); (ii) AMX exposure significantly enhanced the functional pathway genes and beta-lactam resistance genes, and the bloomed pathogens were strongly correlated with the metabolic and immune system diseases gene numbers (R = 0.98, P < 0.001) or bl2_len and bl2be_shv2 abundance (R = 0.94, P < 0.001); (iii) the changes caused by AMX were "SHIME-compartment" different with more significant alteration in ascending colon, and the effects were permanent, which could not be restored after 2-week AMX discontinuance. Overall results demonstrated negative side-effects of AMX, which should be considered for AMX prescription.

Intervention strategies for microbial therapeutics in cancer immunotherapy

Immunotherapies have drastically improved clinical outcomes in a wide range of malignancies. Nevertheless, patient responses remain highly variable, and reliable biomarkers that predict responses accurately are not yet fully understood. Compelling evidence from preclinical studies and observational data from clinical cohorts have shown that commensal microorganisms that reside in the human gastrointestinal tract, collectively termed the ‘microbiome’, can actively modify responses to chemotherapeutic agents and immunotherapies by influencing host immunosurveillance. Notably, microbial correlates are largely context specific, and response signatures may vary by patient population, geographic location and type of anticancer treatment. Therefore, the incongruence of beneficial microbiome signatures across studies, along with an emerging understanding of the mechanisms underlying the interactions between the microbiome, metabolome and host immune system, highlight a critical need for additional comprehensive and standardized multi-omics studies. Future research should consider key host factors, such as diet and use of medication, in both preclinical animal models and large-scale, multicenter clinical trials. In addition, there is a strong rationale to evaluate the microbiome as a tumor-extrinsic biomarker of clinical outcomes and to test the therapeutic potential of derived microbial products (e.g. defined microbial consortia), with the eventual goal of improving the efficacy of existing anticancer treatments. This review discusses the importance of the microbiome from the perspective of cancer immunotherapies, and outlines future steps that may contribute to wide-ranging clinical and translational benefits that may improve the health and quality of life of patients with cancer.

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The gut microbiome impacts the outcomes of cancer treatment by influencing host immunosurveillance.

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Modulation of microbiota represents a novel therapeutic strategy to improve responses.

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Incongruent beneficial bacterial signatures complicate the design of modulators.

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Reverse translation processes can be used to characterize candidate bacteria.

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Rationally designed microbial consortia catalyze transition to a healthy ecology.

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea

Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of "healthy" (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa-function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella, Streptococcus, Dorea, uncultured Lachnospiraceae, Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate "healthy" and "unhealthy" (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

BACKGROUND

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities.

RESULTS

To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities.

CONCLUSIONS

Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.

The Application of Metabolomics to Probiotic and Prebiotic Interventions in Human Clinical Studies

There is an ever-increasing appreciation for our gut microbiota that plays a crucial role in the maintenance of health, as well as the development of disease. Probiotics are live bacteria that are consumed to increase the population of beneficial bacteria and prebiotics are dietary substrates intended to promote the propagation of beneficial bacteria. In order to optimize the use of probiotics and prebiotics, a more complete biochemical understanding of the impact that these treatments have on the community and functioning of the gut microbiota is required. Nucleic acid sequencing methods can provide highly detailed information on the composition of the microbial communities but provide less information on the actual function. As bacteria impart much of their influence on the host through the production of metabolites, there is much to be learned by the application of metabolomics. The focus of this review is on the use of metabolomics in the study of probiotic and prebiotic treatments in the context of human clinical trials. Assessment of the current state of this research will help guide the design of future studies to further elucidate the biochemical mechanism by which probiotics and prebiotics function and pave the way toward more personalized applications.

Using Diverse Model Systems to Define Intestinal Epithelial Defenses to Enteric Viral Infections

The intestine is an essential physical and immunological barrier comprised of a monolayer of diverse and specialized epithelial cells that perform functions ranging from nutrient absorption to pathogen sensing and intestinal homeostasis. The intestinal barrier prevents translocation of intestinal microbes into internal compartments. The microbiota is comprised of a complex community largely populated by diverse bacterial species that provide metabolites, nutrients, and immune stimuli that promote intestinal and organismal health. Although commensal organisms promote health, enteric pathogens, including a diverse plethora of enteric viruses, cause acute and chronic diseases. The barrier epithelium plays fundamental roles in immune defenses against enteric viral infections by integrating diverse signals, including those from the microbiota, to prevent disease. Importantly, many model systems have contributed to our understanding of this complex interface. This review will focus on the antiviral mechanisms at play within the intestinal epithelium and how these responses are shaped by the microbiota.

The microbial exometabolome: ecological resource and architect of microbial communities

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Classical methods and perspectives for manipulating the human gut microbial ecosystem

A healthy Human Gut Microbial Ecosystem (HGME) is a necessary condition for maintaining the orderly function of the whole body. Major alterations in the normal gut microbial composition, activity and functionality (dysbiosis) by an environmental or host-related disruptive event, can compromise metabolic, inflammatory, and neurological processes, causing disorders such as obesity, inflammatory bowel disease, colorectal cancer, and depressive episodes. The restore or the maintaining of the homeostatic balance of Gut Microbiota (GM) populations (eubiosis) is possible through diet, the use of probiotics, prebiotics, antibiotics, and even Fecal Microbiota Transplantation (FMT). Although these "classic methods" represent an effective and accepted way to modulate GM, the complexity of HGME requires new approaches to control it in a more appropriate way. Among the most promising emergent strategies for modulating GM are the use of engineered nanomaterials (metallic nanoparticles (NP), polymeric-NP, quantum dots, micelles, dendrimers, and liposomes); phagotherapy (i.e., phages linked with the CRISPR/Cas9 system), and the use of antimicrobial peptides, non-antibiotic drugs, vaccines, and immunoglobulins. Here we review the current state of development, implications, advantages, disadvantages, and perspectives of the different approaches for manipulating HGME.

Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment

Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.

Gut microbiota in ulcerative colitis: insights on pathogenesis and treatment

Gut microbiota constitute the largest reservoir of the human microbiome and are an abundant and stable ecosystem-based on its diversity, complexity, redundancy, and host interactions This ecosystem is indispensable for human development and health. The integrity of the intestinal mucosal barrier depends on its interactions with gut microbiota. The commensal bacterial community is implicated in the pathogenesis of inflammatory bowel disease (IBD), including ulcerative colitis (UC). The dysbiosis of microbes is characterized by reduced biodiversity, abnormal composition of gut microbiota, altered spatial distribution, as well as interactions among microbiota, between different strains of microbiota, and with the host. The defects in microecology, with the related metabolic pathways and molecular mechanisms, play a critical role in the innate immunity of the intestinal mucosa in UC. Fecal microbiota transplantation (FMT) has been used to treat many diseases related to gut microbiota, with the most promising outcome reported in antibiotic-associated diarrhea, followed by IBD. This review evaluated the results of various reports of FMT in UC. The efficacy of FMT remains highly controversial, and needs to be regularized by integrated management, standardization of procedures, and individualization of treatment.

Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression

If you think you are in control of your behavior, think again. Evidence suggests that behavioral modifications, as development and persistence of depression, maybe the consequence of a complex network of communication between macro and micro-organisms capable of modifying the physiological axis of the host. Some parasites cause significant nutritional deficiencies for the host and impair the effectiveness of cognitive processes such as memory, teaching or non-verbal intelligence. Bacterial communities mediate the establishment of parasites and vice versa but this complexity approach remains little explored. We study the gut microbiota-parasite interactions using novel techniques of network analysis using data of individuals from two indigenous communities in Guerrero, Mexico. Our results suggest that Ascaris lumbricoides induce a gut microbiota perturbation affecting its network properties and also subnetworks of key species related to depression, translating in a loss of emergence. Studying these network properties changes is particularly important because recent research has shown that human health is characterized by a dynamic trade-off between emergence and self-organization, called criticality. Emergence allows the systems to generate novel information meanwhile self-organization is related to the system's order and structure. In this way, the loss of emergence means a depart from criticality and ultimately loss of health.

Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production

Dietary fibers (DFs) impact the gut microbiome in ways often considered beneficial. However, it is unknown if precise and predictable manipulations of the gut microbiota, and especially its metabolic activity, can be achieved through DFs with discrete chemical structures. Using a dose-response trial with three type-IV resistant starches (RS4s) in healthy humans, we found that crystalline and phosphate cross-linked starch structures induce divergent and highly specific effects on microbiome composition that are linked to directed shifts in the output of either propionate or butyrate. The dominant RS4-induced effects were remarkably consistent within treatment groups, dose-dependent plateauing at 35 g/day, and can be explained by substrate-specific binding and utilization of the RS4s by bacterial taxa with different pathways for starch metabolism. Overall, these findings support the potential of using discrete DF structures to achieve targeted manipulations of the gut microbiome and its metabolic functions relevant to health.

Recent advances in modulating the microbiome

We are in the midst of “the microbiome revolution”—not a day goes by without some new revelation on the potential role of the gut microbiome in some disease or disorder. From an ever-increasing recognition of the many roles of the gut microbiome in health and disease comes the expectation that its modulation could treat or prevent these very same diseases. A variety of interventions could, at least in theory, be employed to alter the composition or functional capacity of the microbiome, ranging from diet to fecal microbiota transplantation (FMT). For some, such as antibiotics, prebiotics, and probiotics, an extensive, albeit far from consistent, literature already exists; for others, such as other dietary supplements and FMT, high-quality clinical studies are still relatively few in number. Not surprisingly, researchers have turned to the microbiome itself as a source for new entities that could be used therapeutically to manipulate the microbiome; for example, some probiotic strains currently in use were sourced from the gastrointestinal tract of healthy humans. From all of the extant studies of interventions targeted at the gut microbiome, a number of important themes have emerged. First, with relatively few exceptions, we are still a long way from a precise definition of the role of the gut microbiome in many of the diseases where a disturbed microbiome has been described—association does not prove causation. Second, while animal models can provide fascinating insights into microbiota–host interactions, they rarely recapitulate the complete human phenotype. Third, studies of several interventions have been difficult to interpret because of variations in study population, test product, and outcome measures, not to mention limitations in study design. The goal of microbiome modulation is a laudable one, but we need to define our targets, refine our interventions, and agree on outcomes.

Dietary Patterns Impact Temporal Dynamics of Fecal Microbiota Composition in Children With Autism Spectrum Disorder

Environmental factors such as diet are known influencers on gastrointestinal (GI) microbiota variability and some diseases are associated with microbial stability. Whether microbial variability is related to symptoms of Autism Spectrum Disorder (ASD) and how diet impacts microbial stability in ASD is unknown. Herein, temporal variability in stool microbiota in relation to dietary habits in 2–7 years-old children with ASD (ASD, n = 26) and unaffected controls (CONT, n = 32) was investigated. Fecal samples were collected at baseline, 6-weeks and 6-months. Bacterial composition was assessed using 16S rRNA sequencing. Short fatty acid (SCFA) concentrations were analyzed by gas chromatography. Nutrient intake was assessed using a 3-day food diary and dietary patterns (DP) were empirically derived from a food frequency questionnaire. Social deficit scores (SOCDEF) were assessed using the Pervasive Developmental Disorder Behavior Inventory-Screening Version (PDDBI-SV). GI symptoms were assessed using the GI severity index. Overall, temporal variability in microbial structure, and membership did not differ between the groups. In children with ASD, abundances of Clostridiaceae, Streptophyta, and Clostridiaceae Clostridium, varied significantly, and concentrations of all SCFAs decreased over time. Variability in community membership was negatively correlated with median SOCDEF scores. Additionally, Clostridiales, Lactococcus, Turicibacter, Dorea, and Phascolarctobacterium were components of a more stable microbiota community in children with ASD. DP1, characterized by vegetables, starchy vegetables, legumes, nuts and seeds, fruit, grains, juice and dairy, was associated with changes in species diversity, abundance of Erysipelotricaceae, Clostridiaceae Clostridium, and Oscillospira and concentrations of propionate, butyrate, isobutyrate and isovalerate in children with ASD. DP2 characterized by fried, protein and starchy foods, “Kid's meals,” condiments, and snacks was associated with variations in microbiota structure, abundance of Clostridiaceae Clostridium, and Oscillospira and changes in all SCFA concentrations. However, no association between microbial stability and SOCDEF or GI severity scores were observed. In conclusion, microbiota composition varies over time in children with ASD, might be related to social deficit scores and can be impacted by diet. Future studies investigating the physiological effect of the changes in specific microbial taxa and metabolites are needed to delineate the impact on ASD symptomology.

Inside out: microbiota dynamics during host-plant adaptation of whiteflies

While most insect herbivores are selective feeders, a small proportion of them feed on a wide range of plants. This polyphagous habit requires overcoming a remarkable array of defenses, which often necessitates an adaptation period. Efforts for understanding the mechanisms involved mostly focus on the insect’s phenotypic plasticity. Here, we hypothesized that the adaptation process might partially rely on transient associations with bacteria. To test this, we followed in a field-like experiment, the adaptation process of Bemisia tabaci, a generalist sap feeder, to pepper (a less-suitable host), after switching from watermelon (a suitable host). Amplicon sequencing of 16S rRNA transcripts from hundreds of dissected guts revealed the presence of active “core” and “transient” bacterial communities, dominated by the phyla Proteobacteria, Actinobacteria, and Firmicutes, and increasing differences between populations grown on watermelon and pepper. Insects grown on pepper for over two generations presented a significant increase in specific genera, mainly Mycobacterium, with a predicted enrichment in degradative pathways of xenobiotics and secondary metabolites. This result correlated with a significant increase in the insect’s survival on pepper. Taken together, our findings suggest that gut-associated bacteria can provide an additional flexible metabolic “tool-box” to generalist sap feeders for facilitating a quick host switching process.

Functional microbiome deficits associated with ageing: Chronological age threshold

Composition of the gut microbiota changes during ageing, but questions remain about whether age is also associated with deficits in microbiome function and whether these changes occur sharply or progressively. The ability to define these deficits in populations of different ages may help determine a chronological age threshold at which deficits occur and subsequently identify innovative dietary strategies for active and healthy ageing. Here, active gut microbiota and associated metabolic functions were evaluated using shotgun proteomics in three well-defined age groups consisting of 30 healthy volunteers, namely, ten infants, ten adults and ten elderly individuals. Samples from each volunteer at intervals of up to 6 months (n = 83 samples) were used for validation. Ageing gradually increases the diversity of gut bacteria that actively synthesize proteins, that is by 1.4-fold from infants to elderly individuals. An analysis of functional deficits consistently identifies a relationship between tryptophan and indole metabolism and ageing (p < 2.8e^-8 ). Indeed, the synthesis of proteins involved in tryptophan and indole production and the faecal concentrations of these metabolites are directly correlated (r²  > .987) and progressively decrease with age (r²  > .948). An age threshold for a 50% decrease is observed ca. 11-31 years old, and a greater than 90% reduction is observed from the ages of 34-54 years. Based on recent investigations linking tryptophan with abundance of indole and other "healthy" longevity molecules and on the results from this small cohort study, dietary interventions aimed at manipulating tryptophan deficits since a relatively "young" age of 34 and, particularly, in the elderly are recommended.

Unique and specific Proteobacteria diversity in urinary microbiota of tolerant kidney transplanted recipients

Host-microbiota interactions can modulate the immune system both at local and systemic levels, with potential consequences for organ transplantation outcomes. In this study, we hypothesized that differences in the urinary microbiome following kidney transplantation would be associated with posttransplantation status: stable, minimally immunosuppressed, or tolerant. One hundred thirteen urine samples from stable (n = 51), minimally immunosuppressed (n = 19), and spontaneously tolerant (n = 16) patients, paired with age-matched controls (n = 27) were profiled and compared to each other at a taxonomic level with special interest in the immunosuppressive regimen. All comparisons and correlations were adjusted on sex and time posttransplantation. Our results highlighted a unique and specific urinary microbiota associated with spontaneous tolerance characterized by a high diversity and a clear Proteobacteria profile. Finally, we report that this profile is (1) impacted by gender, (2) inversely correlated with immunosuppressive drugs (calcineurin inhibitors and mammalian target of rapamycin inhibitors), and (3) stable in time.