Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice

Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products

Covering: 1995 to 2023Advances in bioanalytical methods, particularly mass spectrometry, have provided valuable molecular insights into the mechanisms of life. Non-targeted metabolomics aims to detect and (relatively) quantify all observable small molecules present in a biological system. By comparing small molecule abundances between different conditions or timepoints in a biological system, researchers can generate new hypotheses and begin to understand causes of observed phenotypes. Functional metabolomics aims to investigate the functional roles of metabolites at the scale of the metabolome. However, most functional metabolomics studies rely on indirect measurements and correlation analyses, which leads to ambiguity in the precise definition of functional metabolomics. In contrast, the field of natural products has a history of identifying the structures and bioactivities of primary and specialized metabolites. Here, we propose to expand and reframe functional metabolomics by integrating concepts from the fields of natural products and chemical biology. We highlight emerging functional metabolomics approaches that shift the focus from correlation to physical interactions, and we discuss how this allows researchers to uncover causal relationships between molecules and phenotypes.

Exposure to chlorinated drinking water alters the murine fecal microbiota

An abundant body of scientific studies and regulatory guidelines substantiates antimicrobial efficacy of freshwater chlorination ensuring drinking water safety in large populations worldwide. In contrast to the purposeful use of chlorination ensuring antimicrobial safety of drinking water, only a limited body of research has addressed the molecular impact of chlorinated drinking water exposure on the gut microbiota. Here, for the first time, we have examined the differential effects of drinking water regimens stratified by chlorination agent [inorganic (HOCl) versus chloramine (TCIC)] on the C57BL/6J murine fecal microbiota. To this end, we exposed C57BL/6J mice to chlorinated drinking water regimens followed by fecal bacterial microbiota analysis at the end of the three-week feeding period employing 16S rRNA sequencing. α-diversity was strongly reduced when comparing chlorinated versus control drinking water groups and community dissimilarities (β-diversity) were significant between groups even when comparing HOCl and TCIC. We detected significant differences in fecal bacterial composition as a function of drinking water chlorination observable at the phylum and genus levels. Differential abundance analysis of select amplicon sequence variants (ASVs) revealed changes as a function of chlorination exposure [up: Lactobacillus ASV1; Akkermansia muciniphila ASV7; Clostridium ss1 ASV10; down: Ileibacterium valens ASV5; Desulfovibrio ASV11; Lachnospiraceae UCG-006 ASV15]. Given the established complexity of murine and human gastrointestinal microbiota and their role in health and disease, the translational relevance of the chlorination-induced changes documented by us for the first time in the fecal murine microbiota remains to be explored.

2,2-Dichloroacetamide exposure induces behavior and memory disorders in mice: Detrimental effects of long-term dietary restriction on neurotoxicity

2, 2-dichloroacetamide (DCAcAm), a nitrogen-containing disinfection byproduct (DBPs), is commonly found in potable water. This study aimed to compare the neurotoxicity of DCAcAm in C57/BL6 mice at both environmentally relevant and higher doses through oral exposure over a 28-day period. Furthermore, the potential effects of dietary restriction (DR) on the cerebral toxicity induced by 20 ppb DCAcAm were examined. The findings indicated that DCAcAm exposure and DR treatment resulted in reduced memory retention and cognitive adaptability in mice. Additionally, higher doses of DCAcAm exposure induced severe brain inflammation and oxidative stress. Metabolic profiling revealed disruptions in fatty acid, energy, and amino acid metabolism in the brain. Remarkably, the negative impacts of 20 ppb DCAcAm on the mice brain were worsened by DR treatment. Analysis of 16S rRNA sequencing revealed notable changes in the composition and structure of intestinal microorganisms after exposure to DCAcAm. This study discovered that DCAcAm has both direct effects on the brain and indirect effects through the microbial-brain-intestinal axis, which collectively result in neurotoxicity and dietary restriction exacerbates these effects. This study provides emerging views on the assessment of the toxicity of nitrogen containing DBPs.

Impacts of disinfection byproduct exposures on male reproductive health: Current evidence, possible mechanisms and future needs

Disinfection byproducts (DBPs) are a class of ubiquitous chemicals in drinking water and inevitably result in widespread human exposures. Potentially adverse health effects of DBP exposures, including reproductive and developmental outcomes, have been increasing public concerns. Several reviews have focused on the adverse pregnancy outcomes of DBPs. This review summarized current evidence on male reproduction health upon exposure to DBPs from toxicological and epidemiological literature. Based on existing experimental studies, there are sufficient evidence showing that haloacetic acids (HAAs) are male reproductive toxicants, including reduced epididymal weight, decreased semen parameters and sperm protein 22, and declined testosterone levels. However, epidemiological evidence remains insufficient to support a link of DBP exposures with adverse male reproductive outcomes, despite that blood and urinary DBP biomarkers are associated with decreased semen quality. Eight potential mechanisms, including germ/somatic cell dysfunction, oxidative stress, genotoxicity, inflammation, endocrine hormones, folate metabolism, epigenetic alterations, and gut microbiota, are likely involved in male reproductive toxicity of DBPs. We also identified knowledge gaps in toxicological and epidemiological studies to enhance future needs.

Assessing the role of the gut microbiome at the interface between environmental chemical exposures and human health: Current knowledge and challenges

The explosion of microbiome research over the past decade has shed light on the various ways that external factors interact with the human microbiome to drive health and disease. Each individual is exposed to more than 300 environmental chemicals every day. Accumulating evidence indicates that the microbiome is involved in the early response to environmental toxicants and biologically mediates their adverse effects on human health. However, few review articles to date provided a comprehensive framework for research and translation of the role of the gut microbiome in environmental health science. This review summarizes current evidence on environmental compounds and their effect on the gut microbiome, discusses the involved compound metabolic pathways, and covers environmental pollution-induced gut microbiota disorders and their long-term outcomes on host health. We conclude that the gut microbiota may crucially mediate and modify the disease-causing effects of environmental chemicals. Consequently, gut microbiota needs to be further studied to assess the complete toxicity of environmental exposures. Future research in this field is required to delineate the key interactions between intestinal microbiota and environmental pollutants and further to elucidate the long-term human health effects.

DEHP triggers a damage severity grade increase in the jejunum in quail (Coturnix japonica) by disturbing nuclear xenobiotic receptors and the Nrf2-mediated defense response

As a plasticizer, di-2-ethylhexyl phthalate (DEHP) has been listed as a potential endocrine disruptor by The World Health Organization. The toxicity of DEHP has been widely studied, but its toxicity on the digestive tract of birds has not been clarified. Female quail were treated by gavage with DEHP (250, 500, 750 mg/kg), with the blank and vehicle control groups reserved. The result showed that DEHP raised the damage severity grade, and decreased the ratio of villus length to crypt depth. The content and activity of cytochrome P450 system (CYP450s) were increased by DEHP. DEHP interfered with the transcription of nuclear xenobiotic receptors (NXRs), CYP isoforms, and the nuclear factor-E2-related factor 2 (Nrf2) signaling pathway. This study revealed DEHP could cause the imbalance in CYP450s mediated by NXRs, and then promote Nrf2 mediated antioxidant defense. This study provided new evidence about the mechanisms of DEHP-induced toxic effects on digestive tract.

High-performance reductive decomposition of trichloroacetamide by the vacuum-ultraviolet/sulfite process: Kinetics, mechanism and combined toxicity risk

Trichloroacetamide (TCAcAm) is among of the nitrogenous disinfection by-products (N-DBPs) with high cytotoxicity and genotoxicity, which is usually detected at low concentration (μg/L) in drinking water. In this study, advanced reduction process (ARP) based on vacuum ultraviolet (VUV) was employed to eliminate TCAcAm. Compared with VUV, VUV/sulfide, and VUV/ferrous iron processes, VUV/sulfite process demonstrated excellent performance for TCAcAm decomposition, the higher removal of TCAcAm could be achieved by VUV/sulfite process (85.6 %) than VUV direct photolysis (13.5 %) due to the production of a great number of reactive species. The degradation of TCAcAm followed the pseudo-first-order kinetics well in VUV/sulfite process, and the pseudo-first-order rate constant (k_obs) increased with increasing sulfite concentration. Reactive species quenching experiments demonstrated that e_aq^-, SO₃^·- and H· were involved in the degradation of TCAcAm. The in situ generated e_aq^-, SO₃^·- and HO· via VUV/sulfite process were identified by electron paramagnetic resonance (EPR), and the e_aq^- was proved to be the dominated species (relative contribution: 83.5 %) for TCAcAm decomposition. The second-order rate constant of TCAcAm with e_aq^- was determined to be 2.41 × 10¹⁰ M^-1 s^-1 for the first time based on competitive kinetic method. The complete TCAcAm degradation could be achieved at pH > 8.3, while TCAcAm degradation efficiency decreased to 11.9 % at pH 5.8. TCAcAm decay could be divided into two stages: rapid growth (sulfite dosage: 0.25-1.0 mM) and slow growth (sulfite dosage: 1.0-4.0 mM). The yield of e_aq^- was controlled by sulfite dosage, and the predict yield of e_aq^- increased from 3.69 × 10^-14 to 2.58 × 10^-12 M with increasing the sulfite dosage from 0.25 to 4.0 mM by Kintecus 6.80, which resulted in an increase in TCAcAm removal. Meanwhile, the presence of dissolved oxygen (DO), chloride (Cl^-), bicarbonate (HCO₃^-) and humic acid (HA) posed negative influence on TCAcAm decomposition to various degrees. Dichloroacetamide (DCAcAm), trichloroacetic acid (TCAA), dichloroacetic acid (DCAA) and Cl^- were identified as intermediate products, indicated that reductive dechlorination and hydrolysis coexisted during the degradation of TCAcAm in VUV/sulfite process.

Structural and functional alterations of intestinal flora in mice induced by halonitromethanes exposure

Halonitromethanes (HNMs) as one typical class of nitrogenous disinfection byproducts (DBPs) have been widely found in drinking water and are receiving more and more attentions because of their high cytotoxicity, genotoxicity, and developmental toxicity. However, the effects of HNMs exposure on the intestinal tract and intestinal flora remain unknown. This study comprehensively determined the effects of trichloronitromethane, bromonitromethane, and bromochloronitromethane exposure on the intestinal tract and intestinal flora. Results showed that the three HNMs induced intestinal oxidative stress and inflammatory response. Further, HNMs exposure could change the diversities and community structure of intestinal flora, thereby triggering intestinal flora dysbiosis, which might be associated with the intestinal damage such as oxidative stress and inflammation. The intestinal flora dysbiosis was accompanied with mark alterations in function of intestinal flora, such as carbohydrate, lipid, and amino acid metabolisms. This research provides a new insight into studying the toxicity of HNMs exposure based on intestinal flora, which will further improve the health risk assessment of DBPs in drinking water.

Environmental exposure to low-dose perfluorohexanesulfonate promotes obesity and non-alcoholic fatty liver disease in mice fed a high-fat diet

Perfluorohexanesulfonate (PFHxS) is one of the most prevalent perfluoroalkyls. It is widely distributed in both abiotic and biotic environments because of its prevalence and bioaccumulative properties. Exposure to PFHxS has been associated with the higher serum liver functions associated with steatosis in obese people. This study explores the impact of chronic exposure to low-dose PFHxS on predisposition to non-alcoholic fatty liver disease (NAFLD) as well as on metabolic functions in diet-induced obese mice. Results showed that 12-week exposure to PFHxS at a dose of 450 μg/L through drinking water significantly promoted obesity and metabolic syndrome in male C57 mice fed a high-fat diet. The PFHxS exposure markedly aggravated hepatic symptoms resembling NAFLD and caused systematic metabolic disorders as well as gut dysbiosis in the obese mice. Key genes of hepatic lipid metabolism, inflammation, and fibrosis were strongly altered, while gut microflora that have been associated with obesity and pathogenesis of NAFLD, including the Bacteroides/Firmicutes ratio, Desulfovibrio, Mucispirillum, and Akkermansia, were significantly affected by the PFHxS exposure. The findings of this study suggest that environmental PFHxS exposure is a tangible risk factor for metabolic diseases such as NAFLD, especially among obese individuals.

Effects of iodoacetic acid drinking water disinfection byproduct on the gut microbiota and its metabolism in rats

Iodoacetic acid (IAA) is an unregulated disinfection byproduct in drinking water and has been shown to exert cytotoxicity, genotoxicity, tumorigenicity, and reproductive and developmental toxicity. However, the effects of IAA on gut microbiota and its metabolism are still unknown, especially the association between gut microbiota and the metabolism and toxicity of IAA. In this study, female and male Sprague-Dawley rats were exposed to IAA at 0 and 16 mg/kg bw/day daily for 8 weeks by oral gavage. Results of 16S rRNA gene sequencing showed that IAA could alter the diversity, relative abundance and function of gut microbiota in female and male rats. IAA also increased the abundance of genes related to steroid hormone biosynthesis in the gut microbiota of male rats. Moreover, metabolomics profiling revealed that IAA could significantly disturb 6 and 13 metabolites in the feces of female and male rats, respectively. In female rats, the level of androstanediol increased in the IAA treatment group. These results were consistent with our previous findings, where IAA was identified as an androgen disruptor. Additionally, the perturbed gut microbiota and altered metabolites were correlated with each other. The results of this study indicated that IAA could disturb gut microbiota and its metabolism. These changes in gut microbiota and its metabolism were associated with the reproductive and developmental toxicity of IAA.

In vivo toxicity evaluations of halophenolic disinfection byproducts in drinking water: A multi-omics analysis of toxic mechanisms

Halophenolic disinfection byproducts (DBPs) in drinking water have attracted considerable concerns in recent years due to their wide occurrence and high toxicity. The liver has been demonstrated as a major target organ for several halophenolic DBPs. However, little is known about the underlying mechanisms of liver damage caused by halophenolic DBPs. In this study, 2,4,6-trichlorophenol (TCP), 2,4,6-tribromophenol (TBP) and 2,4,6-triiodiophenol (TIP) were selected as representative halophenolic DBPs and exposed to C57BL/6 mice at an environmentally-relevant concentration (0.5 μg/L) and two toxicological concentrations (10 and 200 μg/L) for 12 weeks. Then, a combination of histopathologic and biochemical examination, liver transcriptome, serum metabolome, and gut microbiome was adopted. It was found that trihalophenol exposure significantly elevated the serum levels of alkaline phosphatase and albumin. Liver inflammation was observed at toxicological concentrations in the histopathological examination. Transcriptome results showed that the three trihalophenols could impact immune-related pathways at 0.5 μg/L, which further contributed to the disturbance of pathways in infectious diseases and cancers. Notably, TBP and TIP had higher immunosuppressive effects than TCP, which might lead to uncontrolled infection and cancer. In terms of serum metabolic profiles, energy metabolism pathway of citrate cycle and amino acid metabolism pathways of valine, leucine, and isoleucine were also significantly affected. Integration of the metabolomic and transcriptomic data suggested that a 12-week trihalophenol exposure could prominently disturb the glutathione metabolism pathway, indicating the impaired antioxidation and detoxification abilities in liver. Moreover, the disorder of the intestinal flora could interfere with immune regulation and host metabolism. This study reveals the toxic effects of halophenolic DBPs on mammalian liver and provides novel insights into the underlying mechanisms of hepatotoxicity.

Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.

Immune dysfunction induced by 2,6-dichloro-1,4-benzoquinone, an emerging water disinfection byproduct, due to the defects of host-microbiome interactions

2,6-dichloro-1,4-benzoquinone (DCBQ), as an emerging water disinfection byproducts (DBPs), has posed potential risks via the digestion system. However, little is known about the toxicity of DCBQ on the gut microbiome, which plays a critical role on human health. This study has comprehensively investigated the impact of DCBQ on the intestinal microbiome, metabolic functions, and immunity after the mice orally exposure to DCBQ at the concentration of 31.25, 62.5 and 125 mg/kg body weight for 28 days. Our results indicated that DCBQ exposure has perturbed the balance between T helper (Th) 1 mediated pro-inflammatory response and Th2 mediated anti-inflammatory response in mice, especially inducing the activation of immune system toward a Th2 response. DCBQ group has induced gut microbiota dysbiosis, and at phylum level, Proteobacteria was relatively less abundant compared with that in the control group. Furthermore, DCBQ exposure has dramatically perturbed metabolites profiles which were involved in 28 metabolic pathways, such as amino acids biosynthesis and metabolism, lipid metabolism. In particular, the altered gut microbiota showed strong correlations with both the altered metabolites and the altered immunological variables after DCBQ exposure. This study provides evidence on the adverse effects and mechanisms of water disinfection byproduct DCBQ through the interaction of immune-microbiome-metabolome, highlighting the importance to assess DBPs-associated risks.

Health Effect of N-Nitroso Diethylamine in Treated Water on Gut Microbiota Using a Simulated Human Intestinal Microbiota System

Chlorination disinfection byproducts (CDBPs) can exert adverse human health effects. Many toxicology-based studies confirmed the health hazards of CDBPs, but little research has been done on gut microbiome. We explored the effect of CDBPs on intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The results showed that CDBPs slightly inhibited the production of short-chain fatty acids, and the abundance of Actinobacteria decreased in the transverse colon and descending colon. The abundance of Proteobacteria increased in the ascending colon and descending colon, while it decreased in the transverse colon. The abundance of Firmicutes decreased in both the ascending colon and descending colon. In particular, the abundance of Lachnospiraceae members, Bilophila, Oscillospira, Parabacteroides, Desulfovibrio, and Roseburia increased in the ascending colon, while the abundance of Sutterella, Bacteroides, Escherichia, Phascolarctobacterium, Clostridium, Citrobacter, and Klebsiella increased in the descending colon. The Shannon index differed significantly in both the ascending colon and descending colon before and after exposure. Overall, we demonstrate the feasibility of applying the SHIME model to studying the effects of intestinal toxicity on health of chlorinated by-products. The findings of this study improve our understanding of the health impact of CDBPs on the intestinal microbiota and better control of CDBPs in treated water is recommended.

Diet and Hygiene in Modulating Autoimmunity During the Pandemic Era

The immune system is an efficiently toned machinery that discriminates between friends and foes for achieving both host defense and homeostasis. Deviation of immune recognition from foreign to self and/or long-lasting inflammatory responses results in the breakdown of tolerance. Meanwhile, educating the immune system and developing immunological memory are crucial for mounting defensive immune responses while protecting against autoimmunity. Still to elucidate is how diverse environmental factors could shape autoimmunity. The emergence of a world pandemic such as SARS-CoV-2 (COVID-19) not only threatens the more vulnerable individuals including those with autoimmune conditions but also promotes an unprecedented shift in people's dietary approaches while urging for extraordinary hygiene measures that likely contribute to the development or exacerbation of autoimmunity. Thus, there is an urgent need to understand how environmental factors modulate systemic autoimmunity to better mitigate the incidence and or severity of COVID-19 among the more vulnerable populations. Here, we discuss the effects of diet (macronutrients and micronutrients) and hygiene (the use of disinfectants) on autoimmunity with a focus on systemic lupus erythematosus.

Gut microbiome and metabolic response in non-alcoholic fatty liver disease

Fatty liver disease (FLD) is one of the largest burdens to human health worldwide and is associated with gut microbiome and metabolite stability. Engineered liver tissues have shown promise in restoring liver functions in non-alcoholic FLD (NAFLD), hepatitis and cirrhosis. Fatty liver, largely noted in obesity and hepatic cancer, is highly fatal and has led to a global increase in death rates. It is associated with complex metabolic reprogramming too. A standard approach to therapy in the newly diagnosed setting includes surgery or identification of biomarkers/ metabolites for therapeutic purposes, which ultimately focus on improvement of liver health in patients. As such there are no standard procedures for patient care, but depending on the severity, systemic therapy with either genomic, proteomic or metabolomic profiling form potential options. Better comparisons and study of underlying mechanisms in gut microbiome-based metabolic functions in obesity are urgently required. Today, an emerging field, focusing on metabolomic approaches and metabolic phenotyping, involved in high-throughput identification of metabolome in obesity and gut disorders, is involved in biomarker and metabolite identification. There are supporting technologies and approaches in NAFLD that throw light on the metabolites and gut microbiome, and also on the understanding of the risk factors of obesity along with liver cancer metabolic reaction networks. We discuss the current state of NAFLD metabolites, gut micro-environmental changes, and the further challenges in digital metabolomics profiling. Innovative clinical trial designs, with biomarker-enrichment strategies that are required to improve the outcome of NAFLD in patients are also discussed.

RNase1 can modulate gut microbiota and metabolome after Aeromonas hydrophila infection in blunt snout bream

Pancreatic ribonuclease (RNase1) of Megalobrama amblycephala exhibits both antimicrobial and digestive activity. The gut microbiome improve the digestion and metabolic capacity and enhance the functioning of the immune system of the host against pathogenic bacteria. In this study, we aimed to assess the protective effect of RNase1 on Aeromonas hydrophila-induced inflammation and intestinal microbial metabolism. Megalobrama amblycephala were randomly divided into three groups: control (injected PBS), infection (A. hydrophila-injected), and treatment group (RNase1 pretreatment 24 h before the A. hydrophila injection). The morphological symptoms were significantly alleviated by RNase1. RNase1 reshaped the perturbed gut microbiota by upregulating Proteobacteria and Vibrio richness and downregulating Firmicutes, Chlamydiae, Bacillus, and Gemmobacter richness. The lysophosphatidylcholine, (±) 17 HETE, D- (+) -cellobiose, and PC (20:5) in the treatment group were restored by RNase 1 protein treatment to the level of the control group. In the treatment group, phospholipid metabolism, fatty acid metabolism, glucose metabolism and lipid metabolism were different from the control and infection groups. The proinflammatory factors concentration in intestinal samples significantly increased after A. hydrophila infection. Our results revealed that RNase1 plays an important role in resistance to pathogen invasion, reducing inflammation, and improving intestinal function, thus inhibiting the occurrence of disease.

Extraction optimization for combined metabolomics, peptidomics, and proteomics analysis of gut microbiota samples

Multiomic studies are increasingly performed to gain a deeper understanding of molecular processes occurring in a biological system, such as the complex microbial communities (i.e., microbiota) that reside the distal gut. While a combination of metabolomics and proteomics is more commonly used, multiomics studies including peptidomcis characterization are less frequently undertaken. Here, we investigated three different extraction methods, chosen for their previous use in extracting metabolites, peptides, and proteins, and compared their ability to perform metabolomic, peptidomic, and proteomic analysis of mouse cecum content. The methanol/chloroform/water extraction performed the best for metabolomic and peptidomic analysis as it detected the largest number of small molecules and identified the largest number of peptides, but the acidified methanol extraction performed best for proteomics analysis as it had the highest number of protein identifications. The methanol/chloroform/water extraction was further analyzed by identifying metabolites with tandem mass spectrometry (MS/MS) analysis and by gene ontology analysis for the peptide and protein results to provide a multiomics analysis of the gut microbiota.

Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis

The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.

A Review on the Health Effects of Pesticides Based on Host Gut Microbiome and Metabolomics

Due to their large number of applications, the pesticides pose potential toxicity risks to the non-target organisms. In recent years, the studies on the toxic effects of pesticides on non-target organisms, based on their gut microbiome and metabolome, have been continuously reported. As a dense and diverse microbial community, the gut microbiota in the mammalian gut plays a key role in the maintenance of host metabolic homeostasis. The imbalance in the gut microbiota of host is closely associated with the disturbance in the host's metabolic profile. A comprehensive analysis of the changes in the gut microbiota and metabolic profile of host will help in understanding the internal mechanism of pesticide-induced toxic effects. This study reviewed the composition and function of the gut microbiota of host, as well as the analysis methods and applications of metabolomics. Importantly, the latest research on the toxic effects of the exposure of pesticide to host was reviewed on the basis of changes in their gut microbiota and metabolic profile.

Proinflammatory properties and lipid disturbance of polystyrene microplastics in the livers of mice with acute colitis

Microplastics (MPs) are ubiquitous contaminants in the environment and can be transferred along the food chain, thus causing adverse effects in organisms, even human beings. Therefore, it is of practical importance to identify the environmental risks of MPs, which could lead to a significant impact on public health. In addition to the healthy population, there are large numbers of patients with chronic diseases around the world whose responses to MPs are understudied, representing a significant knowledge gap within the health risk assessment of MPs. In this study, the response sensitivity to MPs of mice with acute colitis was compared with that of healthy mice. The mice were fed water containing polystyrene microplastics (PS MP) at a concentration of 500 μg/L for 28 days. The results showed that PS MP exposure induced inflammatory effects and exerted great disturbance on liver metabolites. Moreover, exposure to PS MP exaggerated dextran sodium sulfate (DSS)-induced acute colitis, as well as lipid disorders, as verified by typical inflammatory factor expression and triglyceride accumulation. The increased intestinal permeability of mice with acute colitis caused by exposure to PS MP may be responsible for the upregulated adverse effects. The results of this study suggest that populations with chronic diseases might be more sensitive to environmental contamination, which should be considered during health risk assessments.

Low-concentration of dichloroacetonitrile (DCAN) in drinking water perturbs the health-associated gut microbiome and metabolic profile in rats

Dichloroacetonitrile (DCAN) is one of the emerging nitrogenous disinfection by-products (DBPs) in drinking water. However, its potential toxicological effects remain poorly understood, especially at a low concentration found in the environment. In the present study, we investigated whether the consumption of low-concentration DCAN through drinking water would produce significant effects in male SD rats, with particular focus on their physiological traits and changes in their gut microbiome and metabolite profiles. After a 4-weeks DCAN intervention, significant changes were observed in the body weight, blood indices, and histology in DCAN-treated (100 μg/L) group. Proteobacteria was relatively less abundant in 20 and 100 μg/L DCAN-treated groups compared with that in the control group at phylum level. At genus level, Parasutterella and Anaerotruncus were significantly less abundant in both 20 and 100 μg/L DCAN-treated groups than that in the control group. Furthermore, the gut microbiota-related metabolites were dramatically perturbed after DCAN consumption. In the 20 and 100 μg/L DCAN-treated groups, there were 48 and 95 altered metabolites, respectively, and were found to be involved in sphingolipid signaling pathway, fatty acid biosynthesis, and cGMP-PKG signaling pathway. In summary, we demonstrated that consumption of low-concentration DCAN through drinking water could impair host health and induce gut microbiota dysbiosis and gut microflora-related metabolic disorders in male SD rats. Our findings highlight the potential toxicity of low-concentration DBPs and provide new insight into potential causal relationship between low concentration DBPs found in the drinking water and the host health.

Oral Exposure to 1,4-Dioxane Induces Hepatic Inflammation in Mice: The Potential Promoting Effect of the Gut Microbiome

1,4-Dioxane is a widely used industrial solvent that has been frequently detected in aquatic environments. However, the hepatotoxicity of long-term dioxane exposure at environmentally relevant concentrations and underlying mechanisms of liver damage remain unclear. In this study, male mice were exposed to dioxane at concentrations of 0.5, 5, 50, and 500 ppm for 12 weeks, followed by histopathological examination of liver sections and multiomics investigation of the hepatic transcriptome, serum metabolome, and gut microbiome. Results showed that dioxane exposure at environmentally relevant concentrations induced hepatic inflammation and caused changes in the hepatic transcriptome and serum metabolic profiles. However, no inflammatory response was observed after in vitro exposure to all concentrations of dioxane and its in vivo metabolites. The gut microbiome was considered to be contributing to this apparently contradictory response. Increased levels of lipopolysaccharide (LPS) may be produced by some gut microbiota, such as Porphyromonadaceae and Helicobacteraceae, after in vivo 500 ppm of dioxane exposure. LPS may enter the blood circulation through an impaired intestinal wall and aggravate hepatic inflammation in mice. This study provides novel insight into the underlying mechanisms of hepatic inflammation induced by dioxane and highlights the need for concerns about environmentally relevant concentrations of dioxane exposure.

Urban-level environmental factors related to pediatric asthma

During the 20th century, urbanization has increasing and represented a major demographic and environmental change in developed countries. This ever-changing urban environment has an impact on disease patterns and prevalence, namely on noncommunicable diseases, such as asthma and allergy, and poses many challenges to understand the relationship between the changing urban environment and the children health. The complex interaction between human beings and urbanization is dependent not only on individual determinants such as sex, age, social or economic resources, and lifestyles and behaviors, but also on environment, including air pollution, indoors and outdoors, land use, biodiversity, and handiness of green areas. Therefore, the assessment and identification of the impact of urban environment on children's health have become a priority and many recent studies have been conducted with the goal of better understanding the impacts related to urbanization, characterizing indoor air exposure, identifying types of neighborhoods, or characteristics of neighborhoods that promote health benefits. Thus, this review focuses on the role of urban environmental factors on pediatric asthma.

Effects of 2,2-dichloroacetamide (DCAcAm), an emerging disinfection by-product in drinking water, on the intestinal microbiota of adult zebrafish

The presence of disinfection by-products (DBPs) increases the mutagenicity of water and may pose adverse health effects. Gut microbiota exerts a fundamental role on host physiology, and how extrinsic perturbations influence its composition has been increasingly examined. However, the effect of DBPs on gut microbiota is still poorly understood. In the present study, adult zebrafish were exposed to different concentrations of dichloroacetamide (DCAcAm, an emerging nitrogenous DBP) for 30 days. Sequencing of 16S rRNA amplicons revealed a significant change in the richness and diversity of microbiota in the gut of DCAcAm-exposed zebrafish. At the phylum level, the abundance of Proteobacteria decreased and the abundance of Fusobacteria and Firmicutes increased significantly in the gut after exposure to 100 and 500 μg/L DCAcAm. At the genus level, the abundances of several bacteria which are considered pathogens or opportunistic pathogens in fish and closely related to fish metabolism, disease and inflammation (Aeromonas, Stenotrophomonas, Bacteroides and Ralstonia) increased in the DCAcAm-treated groups. Our results reveal that DBPs in drinking water potentially affect gut microbiota composition, which may contribute to the toxicity assessment of DBPs in future and provide new insight into the complex interactions between the DBPs in drinking water and host health.

Research progress of disinfection and disinfection by-products in China

Disinfection is an indispensable water treatment process for killing harmful pathogens and protecting human health. However, the disinfection has caused significant public concern due to the formation of toxic disinfection by-products (DBPs). Lots of studies on disinfection and DBPs have been performed in the world since 1974. Although related studies in China started in 1980s, a great progress has been achieved during the last three decades. Therefore, this review summarized the main achievements on disinfection and DPBs studies in China, which included: (1) the occurrence of DBPs in water of China, (2) the identification and detection methods of DBPs, (3) the formation mechanisms of DBPs during disinfection process, (4) the toxicological effects and epidemiological surveys of DBPs, (5) the control and management countermeasures of DBPs in water disinfection, and (6) the challenges and chances of DBPs studies in future. It is expected that this review would provide useful information and reference for optimizing disinfection process, reducing DBPs formation and protecting human health.

Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish

Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.

Boosted TCA cycle enhances survival of zebrafish to Vibrio alginolyticus infection

Vibrio alginolyticus is a waterborne pathogen that infects a wide variety of hosts including fish and human, and the outbreak of this pathogen can cause a huge economic loss in aquaculture. Thus, enhancing host's capability to survive from V. alginolyticus infection is key to fighting infection and this remains still unexplored. In the present study, we established a V. alginolyticus-zebrafish interaction model by which we explored how zebrafish survived from V. alginolyticus infection. We used GC-MS based metabolomic approaches to characterize differential metabolomes between survival and dying zebrafish upon infection. Pattern recognition analysis identified the TCA cycle as the most impacted pathway. The metabolites in the TCA cycle were decreased in the dying host, whereas the metabolites were increased in the survival host. Furthermore, the enzymatic activities of the TCA cycle including pyruvate dehydrogenase (PDH), α-ketoglutaric dehydrogenase (KGDH) and succinate dehydrogenase (SDH) also supported this conclusion. Among the increased metabolites in the TCA cycle, malic acid was the most crucial biomarker for fish survival. Indeed, exogenous malate promoted zebrafish survival in a dose-dependent manner. The corresponding activities of KGDH and SDH were also increased. These results indicate that the TCA cycle is a key pathway responsible for the survival or death in response to infection caused by V. alginolyticus, and highlight the way on development of metabolic modulation to control the infection.

Dietary protein source and butyrylated high-amylose maize starch included in a high-protein diet determines the urinary metabolome of rats

Intake of red and processed meat increases the risk of colorectal cancer (CRC), whereas dairy product consumption and the intake of dietary fibre are negatively associated with this risk. We investigated the effect of (i) low-protein diets with either whey or cooked meat (beef) as the protein source and (ii) high-protein diets with cooked meat (beef) either without or with the inclusion of 10% butyrylated high-amylose maize starch (HAMSB), on the urinary metabolome of rats. Urine samples from rats were analysed using untargeted LC-MS metabolomics. The level and source of the dietary protein affected the urinary excretion of numerous metabolites indicating that several metabolic pathways were changed. The inclusion of HAMSB in a high-protein diet caused significant alterations in the excretion of several metabolites. HAMSB reduced urinary excretion of potentially harmful metabolites resulting from a high level of meat consumption.

Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut

Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.

Urinary Virome Perturbations in Kidney Transplantation

The human microbiome is important for health and plays a role in essential metabolic functions and protection from certain pathogens. Conversely, dysbiosis of the microbiome is seen in the context of various diseases. Recent studies have highlighted that a complex microbial community containing hundreds of bacteria colonizes the healthy urinary tract, but little is known about the human urinary viruses in health and disease. To evaluate the human urinary virome in the context of kidney transplantation (tx), variations in the composition of the urinary virome were evaluated in urine samples from normal healthy volunteers as well as patients with kidney disease after they had undergone kidney tx. Liquid chromatography-mass spectrometry/mass spectrometry analysis was undertaken on a selected cohort of 142 kidney tx patients and normal healthy controls, from a larger biobank of 770 kidney biopsy matched urine samples. In addition to analysis of normal healthy control urine, the cohort of kidney tx patients had biopsy confirmed phenotype classification, coincident with the urine sample analyzed, of stable grafts (STA), acute rejection, BK virus nephritis, and chronic allograft nephropathy. We identified 37 unique viruses, 29 of which are being identified for the first time in human urine samples. The composition of the human urinary virome differs in health and kidney injury, and the distribution of viral proteins in the urinary tract may be further impacted by IS exposure, diet and environmental, dietary, or cutaneous exposure to various insecticides and pesticides.

Altered gut microbiome promotes proteinuria in mice induced by Adriamycin

Inflammation has recently been attributed to dysbiosis of the gut microbiome, which has been linked to proteinuria in chronic kidney disease. Since Adriamycin® (ADR) is widely used to induce proteinuria in mouse models, the aim of this study was to explore the potential effect of gut microbiome on this process. Both ADR resistant (C57BL/6) and susceptible (BALB/C) strains were part of the induced nephropathy with ADR injection. BALB/C mice significantly presented increased urinary albumin/creatinine ratio (UACR) with renal lesions in pathology, but C57BL/6 mice were absent from kidney damage. Species and genus level resolution analysis showed a shift in gut microbial profile between BALB/C and C57BL/6 mice. ADR further altered the stool microbiome in BALB/C mice, particularly with enrichment of Odoribacter and depletion of Turicibacter, Marvinbryantia and Rikenella. Moreover, the level of UACR in BALB/C mice was marked related to the abundance of Marvinbryantia, Odoribacter and Turicibacter in stool. Meanwhile, ADR remarkably increased the serum levels of interleukin (IL)-2 in BALB/C mice, but not in C57BL/6 mice. It is suggested that the favorably altered stools as shown in the microbiome might promote the inflammation and proteinuria in ADR-sensitive mice, which provides a new insight on the pathogenicity of chronic kidney disease.

Effects of exposure to water disinfection by-products in a swimming pool: A metabolome-wide association study

BACKGROUND

Exposure to disinfection by-products (DBPs) in drinking water and chlorinated swimming pools are associated with adverse health outcomes, but biological mechanisms remain poorly understood.

OBJECTIVES

Evaluate short-term changes in metabolic profiles in response to DBP exposure while swimming in a chlorinated pool.

MATERIALS AND METHODS

The PISCINA-II study (EXPOsOMICS project) includes 60 volunteers swimming 40min in an indoor pool. Levels of most common DBPs were measured in water and in exhaled breath before and after swimming. Blood samples, collected before and 2h after swimming, were used for metabolic profiling by liquid-chromatography coupled to high-resolution mass-spectrometry. Metabolome-wide association between DBP exposures and each metabolic feature was evaluated using multivariate normal (MVN) models. Sensitivity analyses and compound annotation were conducted.

RESULTS

Exposure levels of all DBPs in exhaled breath were higher after the experiment. A total of 6,471 metabolic features were detected and 293 features were associated with at least one DBP in exhaled breath following Bonferroni correction. A total of 333 metabolic features were associated to at least one DBP measured in water or urine. Uptake of DBPs and physical activity were strongly correlated and mutual adjustment reduced the number of statistically significant associations. From the 293 features, 20 could be identified corresponding to 13 metabolites including compounds in the tryptophan metabolism pathway.

CONCLUSION

Our study identified numerous molecular changes following a swim in a chlorinated pool. While we could not explicitly evaluate which experiment-related factors induced these associations, molecular characterization highlighted metabolic features associated with exposure changes during swimming.

Systematically investigating the impact of medication on the gut microbiome

In the recent years, there is accumulating evidence for a strong impact of medication on the gut microbiota composition. This evidence comes from metagenomics-based associations and extends beyond classical antibacterials to a handful of human-targeted drugs. To answer whether such effects are direct and explore their consequences in human health, we need to develop experimental platforms that will allow for systematic profiling of drug-microbiota interactions. Here, we discuss approaches, considerations, experimental setups and strategies that can be used to tackle this need, but can be also readily transmitted to related questions in the microbiome field. A comprehensive understanding of how therapeutics interact with gut microbes will open up the path for further mechanistic dissection of such interactions, and ultimately improve not only our understanding of the gut microbiome, but also drug safety and efficacy.

Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata

The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.

A combined NMR- and HPLC-MS/MS-based metabolomics to evaluate the metabolic perturbations and subacute toxic effects of endosulfan on mice

Endosulfan is the newly persistent organic pollutants (POPs) added to the Stockholm Convention as its widespread use, persistence, bioaccumulation, long-range transport, endocrine disruption, and toxicity related to various adverse effects. In the present study, male mice were administrated endosulfan at 0, 0.5, and 3.5 mg/kg by gavage for 2 weeks. ¹H-NMR-based urinary metabolomics, HPLC-MS/MS-based targeted serum metabolomics, clinical analysis, and histopathology techniques were employed to evaluate the metabolic perturbations of subacute endosulfan exposure. Endosulfan exposures resulted in weight loss, liver inflammation and necrosis, and alterations in serum amino acids and urine metabolomics. Based on altered metabolites, several significantly perturbed pathways were identified including glycine, serine, and threonine metabolism; TCA cycle; pyruvate metabolism; glycolysis or gluconeogenesis; glycerophospholipid metabolism; and glyoxylate and dicarboxylate metabolism. Such pathways were highly related to amino acid metabolism, energy metabolism, and lipid metabolism. In addition, metabolomic results also demonstrated that gut microbiota was remarkably altered after endosulfan exposure. These observations may provide novel insight into revealing the potential toxic mechanism and evaluating the health risk of endosulfan exposure at metabolomic level.

Gut Microbiota, Endocrine-Disrupting Chemicals, and the Diabetes Epidemic

Diabetes is rapidly emerging as one of the biggest health concerns worldwide, with profound implications for disability, mortality, and costs. This suddenly escalating rate of diabetes correlates with global industrialization and the production of plastics, pesticides, synthetic fertilizers, electronic waste, and food additives that release endocrine-disrupting chemicals (EDCs) into the environment and the food chain. Emerging evidence indicates an association between exposure of EDCs and diabetes. In humans, these chemicals are also metabolized by the gut microbiota and thereby their toxicodynamics are altered. In this review we highlight studies that focus on the role of gut microbiota in EDC-induced hyperglycemia and dysregulated glucose homeostasis. We also discuss the translational implications of understanding EDC-microbiota interactions for the diagnosis and treatment of diabetes.

Systems Biology to Support Nanomaterial Grouping

The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.

Exploring and Understanding the Biochemical Diversity of the Human Microbiota

Recent studies have illuminated a remarkable diversity and abundance of microbes living on and within the human body. While we are beginning to appreciate associations of certain bacteria and genes with particular host physiological states, considerable information is lacking about the relevant functional activities of the human microbiota. The human gut microbiome encodes tremendous potential for the biosynthesis and transformation of compounds that are important for both microbial and host physiology. Implementation of chemical knowledge and techniques will be required to improve our understanding of the biochemical diversity of the human microbiota. Such efforts include the characterization of novel microbial enzymes and pathways, isolation of microbial natural products, and development of tools to modulate biochemical functions of the gut microbiota. Ultimately, a molecular understanding of gut microbial activities will be critical for elucidating and manipulating these organisms' contributions to human health and disease.

Bacterial Communities: Interactions to Scale

In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

Effects of chlorpyrifos on the gut microbiome and urine metabolome in mouse (Mus musculus)

In this study, the toxic effects of clorpyrifos (CPF) on the gut microbiome and related urine metabolome in mouse (Mus musculus) were investigated. Mice were exposed to a daily dose of 1 mg kg(-1) bodyweight of CPF for 30 d. As a result, CPF significantly altered the gut microbiota composition in terms of the relative abundance of key microbes. Meanwhile, CPF exposure induced the alterations of urine metabolites related to the metabolism of amino acids, energy, short-chain fatty acids (SCFAs), phenyl derivatives and bile acids. High correlations were observed between perturbed gut microbiome and altered metabolic profiles. These perturbations finally resulted in intestinal inflammation and abnormal intestinal permeability, which were also confirm by the histologic changes in colon and remarkable increase of lipopolysaccharide (LPS) and diamine oxidase (DAO) in the serum of CPF-treated mice. Our findings will provide a new perspective to reveal the mechanism of CPF toxicity.

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living organisms. Changes in the microbiome can impact the health of the environmental niche in which they reside. In order to learn more about these communities, different approaches based on data from multiple omics have been pursued. Metagenomics produces a taxonomical profile of the sample, metatranscriptomics helps us to obtain a functional profile, and metabolomics completes the picture by determining which byproducts are being released into the environment. Although each approach provides valuable information separately, we show that, when combined, they paint a more comprehensive picture. We conclude with a review of network-based approaches as applied to integrative studies, which we believe holds the key to in-depth understanding of microbiomes.

Present and foreseeable future of metabolomics in forensic analysis

The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed.

Challenges of metabolomics in human gut microbiota research

The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.

Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State

Obesity resulting from interactions of genetic and environmental factors becomes a serious public health problem worldwide with alterations of the metabolic phenotypes in multiple biological matrices involving multiple metabolic pathways. To understand the contributions of gut microbiota to obesity development, we analyzed dynamic alterations in fecal metabonomic phenotype using NMR and fecal microorganism composition in rats using pyrosequencing technology during the high-fat diet (HFD) feeding for 81 days (pre-obesity state). Integrated analysis of these two phenotypic datasets was further conducted to establish correlations between the altered rat fecal metabonome and gut microbiome. We found that one-week HFD feeding already caused significant changes in rat fecal metabonome and such changes sustained throughout 81-days feeding with the host and gut microbiota co-metabolites clearly featured. We also found that HFD caused outstanding decreases in most fecal metabolites implying enhancement of gut absorptions. We further established comprehensive correlations between the HFD-induced changes in fecal metabonome and fecal microbial composition indicating contributions of gut microbiota in pathogenesis and progression of the HFD-induced obesity. These findings provided essential information about the functions of gut microbiota in pathogenesis of metabolic disorders which could be potentially important for developing obesity prevention and treatment therapies.

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites' abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease.

IMPORTANCE

Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism.