Search

Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mecha-nisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host-parasite-microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics-proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duo-denum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatographic mass-spectrometry, re-spectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome-metabolome analyses indicated that 12 and 16 key pathways were sig-nificantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration in-dicated that populations of three bacterial families –Autopobiaceae (Up), Desulfovibrionaceae (Up) and Akkermanasiaceae (Down) – were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut-liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host-parasite-microbiome biochemical interactions extended beyond the gut ecosystem to the gut-liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host-parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.

Background: The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer’s disease (AD) is poorly understood and the relationships between systemic abnormalities in metabolism and AD/AMCI pathogenesis are unclear. Objective: The aim of the study was to compare the metabolomic and proteomic signature of saliva from cognitively normal and patients diagnosed with MCI or AD, to identify specific cellular pathways altered with the progression of the disease. Methods: We analyzed 80 saliva samples from individuals with MCI or AD as well as age- and gender-matched healthy controls. Saliva proteomic and metabolomic analyses were conducted utilizing mass spectrometry methods and data combined using pathway analysis. Results: We found significant alterations in multiple cellular pathways, demonstrating that at the omics level, disease progression impacts numerous cellular processes. Multivariate statistics using SIMCA showed that partial least squares-data analysis could be used to provide separation of the three groups. Conclusion: This study found significant changes in metabolites and proteins from multiple cellular pathways in saliva. These changes were associated with AD, demonstrating that this approach might prove useful to identify new biomarkers based upon integration of multi-omics parameters.

Functional gastrointestinal disorders (FGID) such as functional dyspepsia (FD) and irritable bowel syndrome (IBS) are highly prevalent and debilitating attributed to altered gut function and gut-brain interactions. FGID can be reliably diagnosed based upon the symptom pattern; but in the clinical setting FD or IBS a frequent diagnoses of exclusion after relevant structural causes of symptoms have been ruled out by appropriate testing. Thus far, there is no established biomarker for FGIDs. To address this limitation, we utilised multi-omics and chemometrics integration to characterise the blood plasma biochemistry in patients with IBS, FD, an overlap of FD/IBS, and controls using liquid chromatography-mass spectrometry (LC-MS) techniques.Cholesterol metabolism products Cholest-5,24-dien-3β-ol, 3-O-β-D-glucopyranoside, energy pathway metabolites, immunoglobulin-γ2 and immunoglobulin-κ, and carbonic anhydrase-1 proteins were particularly elevated in IBS. Furthermore, arginine and proline metabolisms, thyroid hormone synthesis, ferroptosis and, complementary and coagulation cascades were particularly upregulated in patients with IBS. Cer(d18:1/26:1(17Z)) and PI(14:0/22:1(11Z)) lipids were elevated in FD and FD-IBS but were depleted in IBS. Markers of central carbon metabolism and lipidome profiles allowed better discrimination and model predictability than metaproteome profile in healthy and FGID conditions.Overall, the multi-omics integration allowed the discrimination of healthy controls and FGID patients. It also effectively differentiated the biochemistry of FGID subtypes including FD, IBS and FD-IBS co-occurrence. This study points towards the possibility of multi-omics integration for rapid and high throughput analysis of plasma samples to support clinicians screen and diagnose patients with suspected FGIDs.

Background Patients with oral cavity cancer (OCC) and oropharyngeal cancer (OPC) are often seen with locoregionally advanced disease requiring complex multimodality treatments. These treatments may have detrimental effects on the oral microbiome, which is critical to maintaining physiological balance and health.Methods The effects of different OCC and OPC treatment types on the oral microbiome and metabolomic profiles for 24-month post-treatment in patients with OCC and OPC were investigated using 16S rRNA gene amplicon next-generation sequencing and gas chromatography-mass spectrometry (GC-MS), respectively.Results Chemoradiation resulted in oral dysbiosis with specific depletion of genera which regulate the enterosalivary nitrate-nitrite-nitric oxide pathway. These data also correlate with the oral metabolomic profiles with nitric oxide-related precursor, modulator, or catalyst significantly downregulated in saliva samples from patients' postchemoradiation.Conclusions Together, we have shown that oral dysbiosis due to the effects of chemoradiation could potentially have an impact on OCC and OPC patient's quality of life post-treatment.

Insects used to treat organic waste streams and produce valuable protein products are increasingly exposed to plastic contaminated source material assimilating plastic carbon into organic biomass, which is pervasive and hazardous to organisms. Our understanding of this increased insect-plastic interaction remains limited and needs urgent scientific attention if plastic biodegradation and production rates of quality protein are to be improved. Herein, we investigated the biochemical impact of various plastics using three insect models. Black Soldier Fly (BSF), Mealworm (MW), and Wax Moth (WM) larva were each exposed to a plastic substrate (PET, PE, PS, Expanded PE, PP, and PLA) as the primary carbon source for five days to explore any positive metabolic benefits in terms of insect performance and plastic degradation potential. Central carbon metabolism (CCM) metabolites were analyzed via a targeted tMRM liquid chromatography triple quadrupole mass spectrometry (LC-QqQ-MS) method. Unique expressed pathways were observed for each insect model. When reared on PET, BSF larvae were found to have an elevated pyrimidine metabolism, while the purine metabolism pathway was strongly expressed on other plastics. BSF also exhibited a downregulated Vitamin B6 metabolism across all plastics, indicating a likely gut-symbiont breakdown. The MW and WM model insects were metabolically more active on PLA and expanded foam plastics. Further, WM exhibited an elevation in Vitamin B6 metabolism. This data suggests a positive insect-specific interaction towards certain plastic types that warrants further investigation. It is anticipated that through deeper insight into the metabolic impact and benefits afforded from certain plastics, an insect biotransformation pipeline can be established that links fit-for-purpose insect models to individual plastic types that address our growing plastic waste issue.

Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mechanisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host–parasite–microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics–proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duodenum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatography–mass spectrometry, respectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome–metabolome analyses indicated that 12 and 16 key pathways were significantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and the redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration indicated that populations of three bacterial families—Autopobiaceae (Up), Desulfovibrionaceae (Up), and Akkermanasiaceae (Down)—were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut–liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host–parasite–microbiome biochemical interactions extended beyond the gut ecosystem to the gut–liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host–parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.

Purpose The research goal is to develop dietary strategies to help address the growing incidence of inflammatory bowel diseases (IBD). This study has investigated the effectiveness of green banana resistant starch (GBRS) and probiotic Bacillus coagulans MTCC5856 spores for the amelioration of dextran-sulfate sodium (DSS)-induced colitis in mice. Methods Eight-week-old C57BL/6 mice were fed standard rodent chow diet supplemented with either B. coagulans, GBRS or its synbiotic combination. After 7 days supplementation, colitis was induced by adding 2% DSS in drinking water for 7 days while continuing the supplemented diets. Animal health was monitored and after 14 days all animals were sacrificed to measure the biochemical and histochemical changes associated with each supplement type. Results The disease activity index and histological damage score for DSS-control mice (6.1, 17.1, respectively) were significantly higher (p B. coagulans (− 52%, − 58% respectively) or GBRS (− 57%, − 26%, respectively) alone. Compared to DSS-control synbiotic supplementation significantly (p B. coagulans alone could not induce additional levels of short-chain fatty acid (SCFA) production beyond the caecum, the synbiotic combination with GBRS resulted in substantial increased SCFA levels across the whole length of the colon. Conclusion The synbiotic supplementation with B. coagulans and GBRS ameliorated the overall inflammatory status of the experimental IBD model via synergistic functioning. This supports researching its application in mitigating inflammation in human IBD.

Coronavirus disease (COVID-19) is a contagious respiratory disease that is causing significant global morbidity and mortality. Understanding the impact of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection on the host metabolism is still in its infancy but of great importance. Herein, we investigated the metabolic response during viral shedding and post-shedding in an asymptomatic SARS-CoV-2 ferret model (n = 6) challenged with two SARS-CoV-2 isolates. Virological and metabolic analyses were performed on (minimally invasive) collected oral swabs, rectal swabs, and nasal washes. Fragments of SARS-CoV-2 RNA were only found in the nasal wash samples in four of the six ferrets, and in the samples collected 3 to 9 days post-infection (referred to as viral shedding). Central carbon metabolism metabolites were analyzed during viral shedding and post-shedding periods using a dynamic Multiple Reaction Monitoring (dMRM) database and method. Subsequent untargeted metabolomics and lipidomics of the same samples were performed using a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (LC-QToF-MS) methodology, building upon the identified differentiated central carbon metabolism metabolites. Multivariate analysis of the acquired data identified 29 significant metabolites and three lipids that were subjected to pathway enrichment and impact analysis. The presence of viral shedding coincided with the challenge dose administered and significant changes in the citric acid cycle, purine metabolism, and pentose phosphate pathways, amongst others, in the host nasal wash samples. An elevated immune response in the host was also observed between the two isolates studied. These results support other metabolomic-based findings in clinical observational studies and indicate the utility of metabolomics applied to ferrets for further COVID-19 research that advances early diagnosis of asymptomatic and mild clinical COVID-19 infections, in addition to assessing the effectiveness of new or repurposed drug therapies.

Cryptosporidiosis is a major human health concern globally. Despite well-established methods, misdiagnosis remains common. Our understanding of the cryptosporidiosis biochemical mechanism remains limited, compounding the difficulty of clinical diagnosis. Here, we used a systems biology approach to investigate the underlying biochemical interactions in C57BL/6J mice infected with Cryptosporidium parvum. Faecal samples were collected daily following infection. Blood, liver tissues and luminal contents were collected 10 days post infection (dpi). High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of these samples. Faeces and luminal contents were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis of the acquired data illustrated altered host and microbial energy pathways during infection. Glycolysis/citrate cycle metabolites were depleted, while short-chain fatty acids and D-amino acids accumulated. An increased abundance of bacteria associated with a stressed gut environment was seen. Host proteins involved in energy pathways and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase were upregulated during cryptosporidiosis. Liver oxalate also increased during infection. Microbiome-parasite relationships were observed to be more influential than the host-parasite association in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite-microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model towards biomarker discovery, and rapid and accurate diagnostics.

Background Cryptosporidiosis is a major global human health concern. Despite well-established methods, misdiagnosis remain common. Resulting incorrect clinical prescription often causes anti-microbial resistance development in the patients. Our understanding of the Cryptosporidium infection mechanism remains limited, compounding the difficulty of clinical diagnosis. Multi-omics approach has shown significant potential for addressing this limitation and, biomarker discovery towards rapid and accurate diagnostics. This study investigated the underlying biochemistry of host-microbiome-parasite relationships during infection. Methods C57BL/6J mice were infected with 1 × 105 Cryptosporidium parvum oocysts via oral gavage. Faecal samples were collected daily, while blood, liver tissues and luminal contents of the small and large intestines were collected 10 days post infection. High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of faeces, serum, liver, and luminal contents. Faecal samples were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis were applied to all datasets. Results Host and microbial energy pathways altered during infection. Glycolysis/citrate cycle metabolites, such as malate and lactate, were elevated in the large intestine. Short-chain fatty acids, formate and acetate, increased in the small intestine, while butanoate increased in the caecum-colon. This correlated with an increased abundance of bacteria associated with a stressed host environment, including Lactobacillus (small intestine) and Coriobacteriaceae (throughout the intestine, but more prominently in colon). The expression of host electron transfer flavoprotein, phosphoglycerate kinase and acetyl CoA binding proteins, yeast glyceraldehyde-3-phosphate dehydrogenase, and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase significantly increased in the infected gut. Liver oxalate increase was also seen during infection. Conclusions The microbiome-parasite relationship is more influential than the previously thought host-parasite relationship, in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite-microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model.

A probiotic and prebiotic food ingredient combination was tested for synergistic functioning in modulation of the colonic microbiome and remediation of the gastrointestinal immune and inflammatory responses in a spontaneous colitic mouse model. Bacillus coagulans MTCC5856 spores with capability to metabolise complex plant polysaccharides were supplemented with complex whole-plant prebiotic sugarcane fibre (PSCF). The combined and individual efficacies were tested for their influence on the outcomes of chronic inflammation in Muc2 mutant colitic Winnie mice. The mice were fed normal chow diet supplemented with either ingredient or a combination for 21 days. Synbiotic combined supplementation ameliorated clinical symptoms and histological colonic damage scores more effectively than either B. coagulans or PSCF alone. PSCF and B. coagulans alone also induced considerable immunomodulatory effects. Synbiotic supplementation however was the most efficacious in modulating the overall immune profile compared to the unsupplemented Winnie-control. The augmented synbiotic effect could potentially be due to a combination of increased levels of fermentation products, direct immune-modulating abilities of the components, their capability to reduce colonic epithelial damage and/or modulation of the microbiota. The beneficial effects of the supplementation with a complex plant fibre and a fibre-degrading probiotic parallel the effects seen in human microbiota with high plant fibre diets.

The impact of anthropogenic factors arising from point and non-point pollution sources at a multi commodity marine port and its surrounding ecosystems were studied using sediment samples collected from a number of onshore (Gladstone Harbour and Facing Island) and offshore (Heron Island and Fitzroy Reefs) sites in Australia's Central Queensland. Sediment samples were analyzed for trace metals, organic carbon, polycyclic aromatic hydrocarbons (PAH), emerging chemicals of concern (ECC) and sterols. Similarly, the biological and biochemical interaction between the reef and its environment was analyzed by the multi-omic tools of next-generation sequencing characterization of the bacterial community and microbial community metabolic profiling. Overall, the trace elements were observed at the lower end of the Australian environmental guideline values at the offshore sites, while higher values were observed for the onshore locations Nickel and copper were observed above the high trigger value threshold at the onshore sites. The levels of PAH were below limits of detection across all sites. However, some of the ECC and sterols were observed at higher concentrations at both onshore and offshore locations, notably, the cholesterol family sterols and 17α-ethynylestradiol. Multi-omic analyses also indicated possible thermal and photo irradiation stressors on the bacterial communities at all the tested sites. The observed populations of γ-proteobacteria were found in combination with an increased pool of fatty acids that indicate fatty acid synthesis and utilisation of the intermediates of the shikimate pathways. This study demonstrates the value of applying a multi-omics approach for ecological assessments, in which a more detailed assessment of physical and chemical contaminants and their impact on the community bacterial biome is obtained.

Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.

Bivalve molluscs have the potential to bioaccumulate microbial pathogens including noroviruses from aquatic environments and as such, there is a need for a rapid and cheap in-situ method for their detection. Here, we characterise the tissue-specific response of New Zealand Greenshell™ mussels (Perna canaliculus) to faecal contamination from two different sources (municipal sewage and human faeces). This is done with the view to identify potential biomarkers that could be further developed into low cost, rapid and sensitive in-situ biosensors for human faecal contamination detection of mussels in growing areas. Tissue-specific metabolic profiles from gills, haemolymph and digestive glands were analysed using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Clear differentiation of metabolic profiles was observed among treatments in each tissue type. Overall, energy pathways such as glycolysis, citrate cycle and oxidative phosphorylation were downregulated across the three mussel tissues studied following simulated contamination events. Conversely, considerable sterol upregulation in the gills was observed after exposure to contamination. Additionally, free pools of nucleotide phosphates and the antioxidant glutathione declined considerably post-exposure to contamination in gills. These results provide important insights into the tissue-specific metabolic effects of human faecal contamination in mussels. This study demonstrates the utility of metabolomics as a tool for identifying potential biomarkers in mussels.

Background: Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. Methods: The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. Results: Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. Conclusions: Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.

Differentiation between viable and non-viable hookworm ova in environmental samples is necessary in order to implement strategies to mitigate re-infections in endemic regions. In this study, an untargeted metabolic profiling method was developed that utilised gas chromatography-mass spectrometry (GC-MS) in order to investigate hookworm ova viability. Ancylostoma caninum was used to investigate the metabolites within viable and non-viable ova. Univariate and multivariate statistical analyses of the data resulted in the identification of 53 significant metabolites across all hookworm ova samples. The major compounds observed in viable and non-viable hookworm ova were tetradecanoic acid, commonly known as myristic acid [fold change (FC) = 0.4], and dodecanoic acid, commonly known as lauric acid (FC = 0.388). Additionally, the viable ova had self-protecting metabolites such as prostaglandins, a typical feature absent in non-viable ova. The results of this study demonstrate that metabolic profiling using GC-MS methods can be used to determine the viability of canine hookworm ova. Further studies are needed to assess the applicability of metabolic profiling using GC-MS to detect viable hookworm ova in the mixed (viable and non-viable) populations from environmental samples and identify the metabolites specific to human hookworm species.

Microbial-influenced corrosion (MIC) has been known to have economic, environmental, and social implications to offshore oil and gas pipelines, concrete structures, and piped water assets. While corrosion itself is a relatively simple process, the localised manner of corrosion makes in situ assessments difficult. Furthermore, corrosion assessments tend to be measured as part of a forensic investigation. Compounding the issue further is the impact of microbiological/biofilm processes, where corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. While traditional microbiological culture-dependent techniques and electrochemical/physical assessments provide some insight into corrosion activity, the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments are scarce. One avenue to explore MIC and MIC inhibition is through the application of omics-based techniques, where insight into the bacterial population in terms of diversification and their metabolism can be further understood. As such, this paper discusses the recent progresses made in a number of fields that have used omics-based applications to improve the fundamental understanding of biofilms and MIC processes.

Influenza is a highly contagious respiratory disease that causes high global morbidity and mortality each year. The dynamics of an influenza infection on the host metabolism, and how metabolism is altered in response to neuraminidase inhibitor drug therapy, is still in its infancy but of great importance. We aim to investigate the suitability of ferret nasal wash samples for metabolomics-based analysis and characterization of influenza infections and oseltamivir treatment. Virological and metabolic analyses were performed on nasal wash samples collected from ferrets treated with oseltamivir or a placebo. Untargeted metabolomics was performed using a gas chromatography coupled with mass spectrometery (GC-MS) based protocol that comprised a retention time (RT) locked method and the use of a commercial metabolomics library. Ferret activity was reduced at 2–3 days post infection, which coincided with the highest influenza viral titre. The metabolomics data indicated a shift in metabolism during various stages of infection. The neuraminidase inhibitor oseltamivir created considerable downregulation of energy center metabolites (glucose, sucrose, glycine and glutamine), which generated high levels of branched amino acids. This further increased branched amino acid degradation and deregulation via glycerate-type intermediates and biosynthesis of fatty acids in oseltamivir-treated animals where abrogated weight loss was observed. Metabolomics was used to profile influenza infection and antiviral drug treatment in ferrets. This has the potential to provide indicators for the early diagnosis of influenza infection and assess the effectiveness of drug therapies.

Metabolomics is one of the more recently developed "omics" that measures low molecular weight (typically 1500 Da) compounds in biological samples. Metabolomics has been widely explored in environmental, clinical, and industrial biotechnology applications. However, its application to the area of food safety has been limited but preliminary work has demonstrated its value. This chapter describes an untargeted (nontargeted) metabolomics workflow using gas chromatography coupled to mass spectrometry (GC-MS) for characterizing three globally important foodborne pathogens, Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica, from selective enrichment liquid culture media. The workflow involves a detailed description of food spiking experiments followed by procedures for extraction of polar metabolites from media, analyzing the extracts using GC-MS and, finally, chemometric data analysis using the software "SIMCA" to identify potential pathogen-specific biomarkers.

Metabolomics is one of the more recently developed "omics" that measures low molecular weight (typically

Considering the short shelf-life of certain food products such as red meat, there is a need for rapid and cost-effective methods for pathogen detection. Routine pathogen testing in food laboratories mostly relies on conventional microbiological methods which involve the use of multiple selective culture media and long incubation periods, often taking up to 7 days for confirmed identifications. The current study investigated the application of omics-based approaches, proteomics using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) and metabolomics using gas chromatography-mass spectrometry (GC-MS), for detection of three red meat pathogens - Listeria monocytogenes, Salmonella enterica and Escherichia coli O157:H7. Species-level identification was achieved within 18 h for S. enterica and E. coli O157:H7 and 30 h for L. monocytogenes using MALDI-ToF MS analysis. For the metabolomics approach, metabolites were extracted directly from selective enrichment broth samples containing spiked meat samples (obviating the need for culturing on solid media) and data obtained using GC-MS were analyzed using chemometric methods. Putative biomarkers relating to L. monocytogenes, S. enterica and E. coli O157:H7 were observed within 24, 18, and 12 h, respectively, of inoculating meat samples. Many of the identified metabolites were sugars, fatty acids, amino acids, nucleosides and organic acids. Secondary metabolites such as cadaverine, hydroxymelatonin and 3,4-dihydroxymadelic acid were also observed. The results obtained in this study will assist in the future development of rapid diagnostic tests for these important foodborne pathogens.

Fusarium oxysporum has a high affinity for lignin and cellulose-based substrates and is known to grow in a wide range of environments. It is these properties and its ability to produce mycotoxins that have contributed to its pathogenicity in cereal crops that can affect human and animal health when ingested. Identify the mechanisms of mycotoxin production and map the functional output of F. oxysporum under varying growth conditions. Liquid and gas-based chromatography coupled with mass spectrometry was used to identify and map the untargeted metabolic pathway of F. oxysporum grown using nitrogen limited and organic/inorganic nitrogen supplemented media. Over 1300 metabolites were identified, relating to 42 metabolic pathways. Of these, 520 metabolites merged at pyruvate (glycolysis), succinate (Krebs cycle) and aspartate-glutamate metabolic pathways. CoA depletion at the growth stage triggered the initiation of fatty acid and branched amino acid degradation. This in turn activated propionyl CoA carnitine acetyltransferase enzymes, resulting in nitrogen preservation (urea, putrescine and organic acids end-products). CoA then transferred into the TCA cycle via previously unreported β-alanine and propionyl CoA metabolic pathways, the latter likely being a novel methylmalonyl-CoA mutase activity for F. oxysporum. The lower supplementation of inorganic nitrogen compounds (≤ 50 mM) and the elimination of nitrates/organic nitrogen sources resulted in TCA autophagy events that boosted mycotoxin-based metabolism and decreased overall F. oxysporum growth. Such knowledge of functional mycotoxin production can be used to supplement agricultural crops and reduce the risk of mycotoxin contamination in human and animal food supplies.

The application of metabolomics to an ever-greater variety of sample types is a key focus of systems biology research. Recently, there has been a strong focus on applying these approaches toward the rapid analysis of metabolites found in non-invasively acquired samples, such as exhaled breath (also known as 'breathomics'). The sampling process involved in collecting exhaled breath is non-intrusive and comparatively low-cost. It uses a series of globally approved methods and provides researchers with easy access to the metabolites secreted by the human body. Owing to its accuracy and rapid nature, metabolomic analysis of breath is a rapidly growing field that has proven effective in detecting and diagnosing the early stages of numerous diseases and infections. This review discusses the various collection and analysis methods currently applied in breathomics research. Some of the salient research completed in this field to date is also assessed and discussed in order to provide a basis for possible future scientific directions.

Recent evidence suggests that gut microbiota shifts can alter host metabolism even during healthy aging. Lactobacillus acidophilus DDS-1, a probiotic strain, has shown promising probiotic character in vitro, as well as in clinical studies. The present study was carried out to investigate whether DDS-1 can modulate the host metabolic phenotype under the condition of age-affected gut microbial shifts in young and aging C57BL/6J mice. Collected fecal samples were analyzed using 16S rRNA gene sequencing for identifying gut microbiota and untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics analysis. Gut microbial shifts were observed in the control groups (young and aging), leading to an alteration in metabolism. Principal coordinate analysis (PCoA) of microbiota indicated distinct separation in both the DDS-1-treated groups. L. acidophilus DDS-1 increased the relative abundances of beneficial bacteria, such as Akkermansia muciniphila and Lactobacillus spp., and reduced the relative levels of opportunistic bacteria such as Proteobacteria spp. Metabolic pathway analysis identified 10 key pathways involving amino acid metabolism, protein synthesis and metabolism, carbohydrate metabolism, and butanoate metabolism. These findings suggest that modulation of gut microbiota by DDS-1 results in improvement of metabolic phenotype in the aging mice.

BACKGROUND: Ascomycetes are capable of considerable lignocellulose degradation. However, there is limited knowledge on the metabolic profile of their biomass degradation. Metabolomic studies are capable of providing important biochemical information to understand and characterise fungal biomass degradation mechanisms. RESULTS: Winery biomass waste of Vitis vinifera var. Shiraz was subjected to Aspergillus niger mediated solid state fermentation for 8 days in 2H2O supplemented medium. Samples were collected every 24h, freeze-dried and derivatized before GC-MS analysis. Covariance-inverse multivariate statistics were used to classify the most significant metabolites. Metabolite-flux profiling classified 37 unique metabolites in 18 different pathways leading to or from glycolysis-tricarboxylic acid pathways. The majority of the sugars were consumed during the first 4 days; this was in order to synthesize fatty acids, amino acids and secondary metabolites. Inhibition started at day 5, as indicated by the accumulation of sugars and the plateauing of N-acetyl glucosamine (a major fungal cell wall component). CONCLUSIONS: A 4-day continuous yeast or mixed fungal fermentation will not only prevent product inhibition, but it will also aid in generating bio-ethanol. Inducing 2-keto-acid decarboxylases followed alcohol dehydrogenases at the onset of inhibition is predicted to aid in the generation of butanol isomers, which are considered valuable sources of fuel.

Anthropogenic effects of urban density have altered natural ecosystems. Such changes include eutrophication of freshwater and adjoining coastal habitats, and increased levels of inorganic nutrients and pollutants into waterways. In Australia, these changes are intensified by large-scale ocean-atmospheric events, leading to considerable abiotic stress on the natural flora and fauna. Bacterial communities in marine sediments from Moreton Bay (South East Queensland, Australia) were examined in order to assess the impact of rainfall changes, chemical pollution, and subsequent abiotic stress on living organisms within a marine ecosystem. Sediments were collected during the wet and dry seasons and analyzed using bacterial metagenomics and community metabolomics techniques. Physicochemical data were also analyzed to account for biological variance that may be due to non-rainfall-based abiotic stresses. Wet-dry seasonality was the dominant control on bacterial community structure and metabolic function. Changes in the availability of nutrients, organic matter and light appeared to be the major seasonal stressors. In contrast, urban and industrial pollutants appeared to be minor stressors at the sites sampled. During the wet season, the bacterial community composition reflected organisms that utilize biogeochemical pathways with fast kinetics, such as aerobic metabolism, direct assimilation of inorganic compounds, and primary production. The transition to the dry season saw the bacterial community composition shift towards organisms that utilize more complex organic energy sources, such as carbohydrates and fatty acids, and anaerobic redox processes.

BACKGROUND: Recently, winery wastes have been classified as pollutants by the European Union and post-product processing is required to lower their hazards. Individual fungal enzymes have limited capacity so mixed fungal degradation combined with pre-treatment can decrease biomass recalcitrance for more efficient breakdown, overcoming these limitations. RESULTS: Winery biomass degradation by a mixture of Trichoderma harzianum, Aspergillus niger, Penicillium chrysogenum and P. citrinum in submerged fermentation and solid state fermentation (SSF) was evaluated. Higher cellulase and �� -glucosidase activities were observed in SSF and submerged fermentation, respectively. Statistical modelling predicted the fungal percentage ratio of 60:14:4:2 for A. niger: P. chrysogenum: T. harzianum: P citrinum with a substrate:medium ratio of 0.39:1. Under the optimized conditions, cellulase, xylanase and �� -glucosidase activities increased to 78.5, 3544.7 and 250.9 U mL −1 , respectively. Cellulases and xylanases activities increased more than two-fold. Lignin degradation increased from 8% in submerged fermentation (P. chrysogenum) to 17.9% under optimized conditions. Gas chromatography–mass spectrometry (GC-MS) analysis identified 78 significant metabolites, of which stigmasterol, glycerol, maleic acid, xylitol and citric acid were generated by fungal degradation.

a b s t r a c t Hydrothermal-treated (autoclaved) winery waste was degraded by Trichoderma harzianum, Aspergillus niger, Penicillium chrysogenum and Penicillium citrinum. Quantification of lignins, reducing sugars, pentoses and enzyme assays for cellulase, -glucosidase and xylanase were performed. Lignin content increased from 36% in untreated waste to 63% in autoclaved substrate. Lignin degradation of 9% and 4.2% was achieved by P. chrysogenum and A. niger, respectively. Reducing sugars decreased by 1.2 and 0.7 kg/m3 in T. harzianum and P. citrinum cultures, respectively. Pentose utilization was also considerable across all cultures. Cellulase and xylanase activities were higher in A. niger cultures at 45 U and 335 U, respectively. It also showed high -glucosidase activity of 155 U, marginally less than P. citrinum (180 U). Autoclaving hydrolyzed hemicelluloses and crystalline cellulose, converting the latter to a more degradable amorphous form. The results suggest that successive hydrothermal and fungal treatments produce greater lignocellulose degradation than regular fermentation.

Distribution of the microbiota varies according to the location in the gastrointestinal (GI) tract. Thus, dysbiosis during aging may not be limited to faecal microbiota and extend to the other parts of the GI tract, especially the cecum and colon. Lactobacillus acidophilus DDS-1, a probiotic strain, has been shown to modulate faecal microbiota and its associated metabolic phenotype in aging mice. In the present study, we investigated the effect of L. acidophilus DDS-1 supplementation on caecal- and mucosal-associated microbiota, short-chain fatty acids (SCFAs) and immunological profiles in young and aging C57BL/6J mice. Besides differences in the young and aging control groups, we observed microbial shifts in caecal and mucosal samples, leading to an alteration in SCFA levels and immune response. DDS-1 treatment increased the abundances of beneficial bacteria such as Akkermansia spp. and Lactobacillus spp. more effectively in caecal samples than in mucosal samples. DDS-1 also enhanced the levels of butyrate, while downregulating the production of inflammatory cytokines (IL-6, IL-1&beta, IL-1&alpha, MCP-1, MIP-1&alpha, MIP-1&beta, IL-12 and IFN-&gamma, ) in serum and colonic explants. Our findings suggest distinct patterns of intestinal microbiota, improvements in SCFA and immunological profiles with DDS-1 supplementation in aging mice.

To increase the efficiency of winery-derived biomass biodegradation, grape pomace was ultrasonicated for 20min in the presence of 0.25M, 0.5Mand1.0MKOH and 1.0MNaOH. This was followed by treatment with a 1:1 (v/v) mix of crude enzyme preparation derived from Phanerochaete chrysosporium and Trametes versicolor for 18h and a further 18h treatment with a 60:14:4:2 percent ratio combination of enzymes derived from Aspergillus niger: Penicillium chrysogenum: Trichoderma harzianum: P. citrinum, repsectively. Process efficiency was evaluated by its comparison to biological only mixed fungal degradation over 16days. Ultrasonication treatment with 0.5MKOH followed by mixed enzyme treatment yielded the highest lignin degradation of about 13%. Cellulase, β-glucosidase, xylanase, laccase and lignin peroxidase activities of 77.9, 476, 5,390.5, 66.7 and 29,230.7U/mL, respectively, were observed during biomass degradation. Gas chromatography-mass spectrometry (GC-MS) analysis of the degraded material identified commercially important compounds such as gallic acid, lithocholic acid, glycolic acid and lactic acid which were generated in considerable quantities. Thus, the combination of sonication pre-treatment and enzymatic degradation has the potential to considerably improve the breakdown of agricultural biomass and produce commercially useful compounds in markedly less time (

Agricultural processes, especially harvesting and post-harvesting, generate considerable amounts of biomass waste every year, the majority of which is incinerated or ends up in landfill. However, this biomass has, instead, the potential to be utilised for various applications including the production of biofuels and numerous medicinal and important industrial metabolites. Numerous bacteria, especially thermophilic species, and fungi have the ability to degrade complex biomass substrates to simpler, useful products which have wide commercial applications. The wide variability in biomass composition and the low degradation capability of individual microbes, however, has limited the utilisation of these wastes. In recent years, the field of metabolomics has been successfully applied to identify the many limiting factors of bioconversion processes. Metabolic profiling has also helped to identify the critical points in microbial metabolic pathways to not only overcome these limiting factors, but also increase the production of valuable by-products products. This chapter reviews the application of microbial metabolomics to increase the efficiency of biomass degradation. It will describe recent advances and future aspects of microbial metabolite profiling and metabolic engineering processes to optimise the production of various compounds of medicinal and industrial interest.

Genomics and transcriptonomics studies have been the cornerstones of numerous biological progresses in several decades. Additionally, proteomic studies, especially related to clinical studies have been popular since 1970s. In last decade, owing to technological advances, considerable progress has been made in the metabolic studies of several biological phenomena, ranging from clinical to environmental studies. Since the advent of the Human Genome consortium in the 1990s, there has been an exponential progress in the studies of not only genomics (and metagenomics), but also transcriptomics and proteomics. A rapid rise in metabolomics and its complementation to the former researches has necessitated the combination of all these techniques to obtain a broader picture of the biological system. A combination study, broadly termed as ‘Multi-omics’ has been a field of interest since 2008. A ‘multi-omics’ approach combines major fields such as genomics, transcriptomics, proteomics and metabolomics, in addition to minor omics-based approaches such as fluxomics, ionomics and lipidomics (among others) in order to obtain elaborate knowledge of an entire biological system, in a single study. This chapter discusses the progress of multi-omics in recent years and presents some case studies in multiple fields such as human health, the environment, industrial biotechnology and biofuel studies among others. The chapter also discusses the development of various analytical methods and databases in multi-omics, with tentative future trends in the field.

In this study, laboratory scale digesters were operated to simulate potential shocks to the Anaerobic Digestion (AD) process at a 350 ML/day wastewater treatment plant. The shocks included high (42 °C) and low (32 °C) temperature (either side of mesophilic 37 °C) and a 20% loading of fats, oil and grease (FOG; 20% w:v). These variables were explored at two sludge retention times (12 and 20 days) and two organic loading rates (2.0 and 2.5 kgTS/m(3)day OLR). Metagenomic and metabolomic approaches were then used to characterise the impact of operational shocks in regard to temperature and FOG addition, as determined through monitoring of biogas production, the microbial profile and their metabolism. Results showed that AD performance was not greatly affected by temperature shocks, with the biggest impact being a reduction in biogas production at 42 °C that persisted for 32 ± 1 days. The average biogas production across all digesters at the completion of the experiment was 264.1 ± 76.5 mL/day, with FOG addition observed to significantly promote biogas production (+87.8 mL/day). Metagenomic and metabolomic analyses of the digesters indicated that methanogens and methane oxidising bacteria (MOB) were low in relative abundance, and that the ratio of oxidising bacteria (methane, sulphide and sulphate) with respect to sulphate reducing bacteria (SRB) had a noticeable influence on biogas production. Furthermore, increased biogas production correlated with an increase in short chain fatty acids, a product of the addition of 20% FOG. This work demonstrates the application of metagenomics and metabolomics to characterise the microbiota and their metabolism in AD digesters, providing insight to the resilience of crucial microbial populations when exposed to operational shocks.

This paper illustrates the application of an untargeted metabolic profiling analysis of winery-derived biomass degraded using four filamentous fungi (Trichoderma harzianum, Aspergillus niger, Penicillium chrysogenum and P. citrinum) and a yeast (Saccharomyces cerevisiae). Analysis of the metabolome resulted in the identification of 233 significant peak features [P0.05; fold change (FC)2 and signal-to-noise ratio50] using gas chromatography-mass spectrometry followed by statistical chemometric analysis. Furthermore, A. niger and P. chrysogenum produced higher biomass degradation due to considerable β-glucosidase and xylanase activities. The major metabolites generated during fungal degradation which differentiated the metabolic profiles of fungi included sugars, sugar acids, organic acids and fatty acids. Although, P. chrysogenum could degrade hemicelluloses due to its high β-glucosidase and xylanase activities, it could not utilize the resultant pentoses, which A. niger and P. citrinum could do efficiently, thus indicating a need of mixed fungal culture to improve the biomass degradation. Saccharomyces cerevisiae, a non-cellulose degrader, exhibited sugar accumulation during the fermentation. Penicillium chrysogenum was observed to degrade about 2% lignin, a property not observed in other fungi. This study emphasized the differential fungal metabolic behavior and demonstrated the potential of metabolomics in optimizing degradation or manipulating pathways to increase yields of products of interest.