Publications by authors named "Emma Allen-Vercoe"

87 Publications

Commensals make the most of their hosts.

Cell Host Microbe 2021 Sep;29(9):1337-1339

Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada. Electronic address:

In this issue of Cell Host & Microbe, Brown et al. reveal a large group of genes within the human microbiome that code for ADP-ribosyltransferases that are predicted to manipulate host cells. Previously studied for pathogens, these host modification mechanisms may also be common properties of commensals.
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http://dx.doi.org/10.1016/j.chom.2021.08.007DOI Listing
September 2021

Culturing Human Gut Microbiomes in the Laboratory.

Annu Rev Microbiol 2021 May 26. Epub 2021 May 26.

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; email:

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the , Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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http://dx.doi.org/10.1146/annurev-micro-031021-084116DOI Listing
May 2021

Bioactive small molecules produced by the human gut microbiome modulate sessile and planktonic lifestyles.

Gut Microbes 2021 Jan-Dec;13(1):1-19

Instituto Nacional de Ciência e Tecnologia de Inovação Em Doenças De Populações Negligenciadas, Centro De Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.

Humans live in symbiosis with a diverse community of microorganisms, which has evolved to carry out many specific tasks that benefit the host, including protection against invading pathogens. Within the chemical diversity of the gastrointestinal tract, small molecules likely constitute chemical cues for the communication between the microbiota and pathogens. Therefore, we sought to investigate if molecules produced by the human gut microbiota show biological activity against the human pathogen . To probe the effects of the gut metabolome on , we investigated its response to small-molecule extracts from human feces, from a complex bacterial community cultivated , and from culture supernatants of , and . Using RNA sequencing, we determined the impact of the human gut metabolome on global gene expression. Among the genes downregulated in the presence of the fecal extract, the most overrepresented functional category was cell motility, which accounted for 39% of repressed genes. Repression of motility by the fecal extract was confirmed phenotypically, and extracts reproduced this phenotype. A complex microbial community led to increased motility, as did extracts from , a species present in this community. Accordingly, mucin penetration was also repressed by fecal and extracts, suggesting that the phenotypes observed may have implications for host colonization. Together with previous studies, this work shows that small molecules from the gut metabolome may have a widespread, significant impact on microbe-microbe interactions established in the gut environment.
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http://dx.doi.org/10.1080/19490976.2021.1918993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143261PMC
May 2021

Anaerobes in the microbiome.

Anaerobe 2021 Apr;68:102362

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

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http://dx.doi.org/10.1016/j.anaerobe.2021.102362DOI Listing
April 2021

Defined gut microbial communities: promising tools to understand and combat disease.

Microbes Infect 2021 Jul-Aug;23(6-7):104816. Epub 2021 Mar 27.

Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. Electronic address:

Defined gut microbial communities are emerging tools that allow detailed studies of microbial ecosystems and their interactions with the host. In this article, we review strategies underlying the design of defined consortia and summarize the efforts to introduce simplified communities into in vitro and in vivo models. We conclude by highlighting the potential of defined microbial ecosystems as effective modulation strategies for health benefits.
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http://dx.doi.org/10.1016/j.micinf.2021.104816DOI Listing
March 2021

The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial.

Lancet Gastroenterol Hepatol 2021 04 23;6(4):282-291. Epub 2021 Feb 23.

NuBiyota, University of Guelph, Guelph, ON, Canada; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.

Background: Faecal microbiota transplantation (FMT) is highly effective for recurrent Clostridioides difficile infection but has inherent risks. Microbial Ecosystem Therapeutic 2 (MET-2) is an oral encapsulated formulation of 40 lyophilised bacterial species initially isolated from stool of a healthy donor, but subsequently manufactured independently of donors, eliminating potential risks introduced by changes in donor health. The aim of this study was to determine MET-2 activity, safety, and tolerability.

Methods: This phase 1, open-label, single-group feasibility study was done in Alberta, Canada. The main inclusion criteria were mild to moderate C difficile infection and at least one episode of C difficile infection recurrence (ie, two episodes of C difficile infection) within 12 months. Initial daily treatment was ten oral capsules for 2 days, then three capsules for 8 days. If C difficile infection recurred, a higher dose was offered: 20 capsules for 2 days, then three capsules for 8 days. Patients were followed for adverse events and C difficile infection recurrence up to day 130. The primary outcome was absence of C difficile infection recurrence (fewer than three unformed bowel movements in 24 h persisting for at least 2 days) at day 40 by intention-to-treat analysis. Secondary outcomes were mortality or hospitalisation due to C difficile infection, infections attributed to treatment, nausea, abdominal pain, vomiting, or diarrhoea during treatment, quality of life (C difficile Health Related Quality of Life Questionnaire) before and after treatment, and engrafted MET-2 bacteria in patient stool. Absence of C difficile infection recurrence at day 130 was an exploratory outcome. This study is registered with ClinicalTrials.gov, NCT02865616 FINDINGS: Between Sept 19, 2018, and Feb 28, 2020, we enrolled 19 adult patients with at least two episodes of mild to moderate C difficile infection (median age 65 years [IQR 56-67]; 12 women [63%], seven men [37%]). Recurrent C difficile infection was absent at day 40 in 15 (79%) of 19 patients after initial treatment, increasing to 18 (95%) 40 days after retreatment. No mortality associated with C difficile infection, infections associated with MET-2 treatment, or other serious adverse events were observed. The most common self-limited, mild to moderate symptoms reported during treatment were diarrhoea in 12 (63%) of 19 patients and abdominal cramps in 12 (63%). After MET-2 treatment, quality of life improved significantly, as did alpha diversity in stool microbial composition (p=1·93×10). MET-2 associated taxa were found in greater abundance in most patients after treatment compared with baseline. 16 (84%) of 19 patients did not have recurrence of C difficile infection by day 130.

Interpretation: MET-2 appears to be safe, efficacious, and well tolerated among patients with recurrent C difficile infection. Results must be validated in controlled studies.

Funding: NuBiyota.
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http://dx.doi.org/10.1016/S2468-1253(21)00007-8DOI Listing
April 2021

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.

Nat Commun 2020 12 15;11(1):6389. Epub 2020 Dec 15.

ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
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http://dx.doi.org/10.1038/s41467-020-19929-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7738495PMC
December 2020

A Microbiota-Derived Metabolite Augments Cancer Immunotherapy Responses in Mice.

Cancer Cell 2020 10 24;38(4):452-453. Epub 2020 Sep 24.

University Hospital Network, Division of Infectious Diseases and Toronto General Hospital Research Institute, Division of Advanced Diagnostics, 101 College Street, Toronto, ON M5G 1L7, Canada. Electronic address:

Improving the rate of patient response to immune checkpoint blockade therapy is a current clinical goal. An article published in Science suggests that some members of the gut microbiome may provide a key molecule toward this end.
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http://dx.doi.org/10.1016/j.ccell.2020.09.005DOI Listing
October 2020

Circadian influence on the microbiome improves heart failure outcomes.

J Mol Cell Cardiol 2020 12 19;149:54-72. Epub 2020 Sep 19.

Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada. Electronic address:

Myocardial infarction (MI) leading to heart failure (HF) is a major cause of death worldwide. Previous studies revealed that the circadian system markedly impacts cardiac repair post-MI, and that light is an important environmental factor modulating the circadian influence over healing. Recent studies suggest that gut physiology also affects the circadian system, but how it contributes to cardiac repair post-MI and in HF is not well understood. To address this question, we first used a murine coronary artery ligation MI model to reveal that an intact gut microbiome is important for cardiac repair. Specifically, gut microbiome disruption impairs normal inflammatory responses in infarcted myocardium, elevates adverse cardiac gene biomarkers, and leads to worse HF outcomes. Conversely, reconstituting the microbiome post-MI in mice with prior gut microbiome disruption improves healing, consistent with the notion that normal gut physiology contributes to cardiac repair. To investigate a role for the circadian system, we initially utilized circadian mutant Clock mice, revealing that a functional circadian mechanism is necessary for gut microbiome benefits on post-MI cardiac repair and HF. Finally, we demonstrate that circadian-mediated gut responses that benefit cardiac repair can be conferred by time-restricted feeding, as wake time feeding of MI mice improves HF outcomes, but these benefits are not observed in MI mice fed during their sleep time. In summary, gut physiology is important for cardiac repair, and the circadian system influences the beneficial gut responses to improve post-MI and HF outcomes.
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http://dx.doi.org/10.1016/j.yjmcc.2020.09.006DOI Listing
December 2020

1D H NMR as a Tool for Fecal Metabolomics.

Curr Protoc Chem Biol 2020 09;12(3):e83

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

Metabolomic studies allow a deeper understanding of the processes of a given ecological community than nucleic acid-based surveys alone. In the case of the gut microbiota, a metabolic profile of, for example, a fecal sample provides details about the function and interactions within the distal region of the gastrointestinal tract, and such a profile can be generated in a number of different ways. This unit elaborates on the use of 1D H NMR spectroscopy as a commonly used method to characterize small-molecule metabolites of the fecal metabonome (meta-metabolome). We describe a set of protocols for the preparation of fecal water extraction, storage, scanning, measurement of pH, and spectral processing and analysis. We also compare the effects of various sample storage conditions for processed and unprocessed samples to provide a framework for comprehensive analysis of small molecules from stool-derived samples. © 2020 Wiley Periodicals LLC Basic Protocol 1: Extracting fecal water from crude fecal samples Alternate Protocol 1: Extracting fecal water from small crude fecal samples Basic Protocol 2: Acquiring NMR spectra of metabolite samples Alternate Protocol 2: Acquiring NMR spectra of metabolite samples using Bruker spectrometer running TopSpin 3.x Alternate Protocol 3: Acquiring NMR spectra of metabolite samples by semiautomated process Basic Protocol 3: Measuring sample pH Support Protocol 1: Cleaning NMR tubes Basic Protocol 4: Processing raw spectra data Basic Protocol 5: Profiling spectra Support Protocol 2: Spectral profiling of sugars and other complex metabolites.
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http://dx.doi.org/10.1002/cpch.83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7968567PMC
September 2020

Corrigendum to Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 Jul 25;224:103829. Epub 2020 May 25.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2020.103829DOI Listing
July 2020

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.

Cell Host Microbe 2020 06 28;27(6):1001-1013.e9. Epub 2020 Apr 28.

Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.
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http://dx.doi.org/10.1016/j.chom.2020.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292766PMC
June 2020

Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities.

J Proteomics 2020 06 23;222:103791. Epub 2020 Apr 23.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany. Electronic address:

Stable isotope probing (SIP) approaches are a suitable tool to identify active organisms in bacterial communities, but adding isotopically labeled substrate can alter both the structure and the functionality of the community. Here, we validated and demonstrated a substrate-independent protein-SIP protocol using isotopically labeled water that captures the entire microbial activity of a community. We found that O yielded a higher incorporation rate into peptides and thus comprised a higher sensitivity. We then applied the method to an in vitro model of a human distal gut microbial ecosystem grown in two medium formulations, to evaluate changes in microbial activity between a high-fiber and high-protein diet. We showed that only little changes are seen in the community structure but the functionality varied between the diets. In conclusion, our approach can detect species-specific metabolic activity in complex bacterial communities and more specifically to quantify the amount of amino acid synthesis. Heavy water makes possible to analyze the activity of bacterial communities for which adding an isotopically labeled energy and nutrient sources is not easily feasible. SIGNIFICANCE: Heavy stable isotopes allow for the detection of active key players in complex ecosystems where many organisms are thought to be dormant. Opposed to the labelling with energy or nutrient sources, heavy water could be a suitable replacement to trace activity, which has been shown for DNA and RNA. Here we validate, quantify and compare the incorporation of heavy water either labeled with deuterium or 18‑oxygen into proteins of Escherichia coli K12 and of an in vitro model of a human gut microbial ecosystem. The significance of our research is in providing a freely available pipeline to analyze the incorporation of deuterium and 18‑oxygen into proteins together with the validation of the applicability of tracing heavy water as a proxy for activity. Our approach unveils the relative functional contribution of microbiota in complex ecosystems, which will improve our understanding of both animal- and environment-associated microbiomes and in vitro models.
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http://dx.doi.org/10.1016/j.jprot.2020.103791DOI Listing
June 2020

Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics.

Expert Rev Proteomics 2020 02 15;17(2):163-173. Epub 2020 Mar 15.

Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.

: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.
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http://dx.doi.org/10.1080/14789450.2020.1738931DOI Listing
February 2020

Protease-dependent excitation of nodose ganglion neurons by commensal gut bacteria.

J Physiol 2020 06 6;598(11):2137-2151. Epub 2020 Apr 6.

Gastrointestinal Disease Research Unit (GIDRU), Queen's University, Kingston, Ontario, K7L2V7, Canada.

Key Points: The vagus nerve has been implicated in mediating behavioural effects of the gut microbiota on the central nervous system. This study examined whether the secretory products of commensal gut bacteria can modulate the excitability of vagal afferent neurons with cell bodies in nodose ganglia. Cysteine proteases from commensal bacteria increased the excitability of vagal afferent neurons via activation of protease-activated receptor 2 and modulation of the voltage dependence of Na conductance activation. Lipopolysaccharide, a component of the cell wall of gram-negative bacteria, increased the excitability of nodose ganglia neurons via TLR4-dependent activation of nuclear factor kappa B. Our study identified potential mechanisms by which gut microbiota influences the activity of vagal afferent pathways, which may in turn impact on autonomic reflexes and behaviour.

Abstract: Behavioural studies have implicated vagal afferent neurons as an important component of the microbiota-gut-brain axis. However, the mechanisms underlying the ability of the gut microbiota to affect vagal afferent pathways are unclear. We examined the effect of supernatant from a community of 33 commensal gastrointestinal bacterial derived from a healthy human donor (microbial ecosystem therapeutics; MET-1) on the excitability of mouse vagal afferent neurons. Perforated patch clamp electrophysiology was used to measure the excitability of dissociated nodose ganglion (NG) neurons. NG neuronal excitability was assayed by measuring the amount of current required to elicit an action potential, the rheobase. MET-1 supernatant increased the excitability of NG neurons by hyperpolarizing the voltage dependence of activation of Na conductance. The increase in excitability elicited by MET-1 supernatant was blocked by the cysteine protease inhibitor E-64 (30 nm). The protease activated receptor-2 (PAR ) antagonist (GB 83, 10 μm) also blocked the effect of MET-1 supernatant on NG neurons. Supernatant from Lactobacillus paracasei 6MRS, a component of MET-1, recapitulated the effect of MET-1 supernatant on NG neurons. Lastly, we compared the effects of MET-1 supernatant and lipopolysaccharide (LPS) from Escherichia coli 05:B5 on NG neuron excitability. LPS increased the excitability of NG neurons in a toll-like receptor 4 (TLR )-dependent and PAR -independent manner, whereas the excitatory effects of MET-1 supernatant were independent of TLR activation. Together, our findings suggest that cysteine proteases from commensal bacteria increase the excitability of vagal afferent neurons by the activation of PAR .
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http://dx.doi.org/10.1113/JP279075DOI Listing
June 2020

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria .

mSystems 2020 Jan 28;5(1). Epub 2020 Jan 28.

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

Fecal microbiota transplantation (FMT) is a proposedly useful strategy for the treatment of gastrointestinal (GI) disorders through remediation of the patient gut microbiota. However, its therapeutic success has been variable, necessitating research to uncover mechanisms that improve patient response. Antibiotic pretreatment has been proposed as one method to enhance the success rate by increasing niche availability for introduced species. Several limitations hinder exploring this hypothesis in clinical studies, such as deleterious side effects and the development of antimicrobial resistance in patients. Thus, the purpose of this study was to evaluate the use of an , bioreactor-based, colonic ecosystem model as a form of preclinical testing by determining how pretreatment with the antibiotic rifaximin influenced engraftment of bacterial strains sourced from a healthy donor into an ulcerative colitis-derived defined microbial community. Distinct species integrated under the pretreated and untreated conditions, with the relative rifaximin resistance of the microbial strains being an important influencer. However, both conditions resulted in the integration of taxa from clusters IV and XIVa, a concomitant reduction of , and similar decreases in metabolites associated with poor health status. Our results agree with the findings of similar research in the clinic by others, which observed no difference in primary patient outcomes whether or not patients were given rifaximin prior to FMT. We therefore conclude that our model is useful for screening for antibiotics that could improve efficacy of FMT when used as a pretreatment. Patients with gastrointestinal disorders often exhibit derangements in their gut microbiota, which can exacerbate their symptoms. Replenishing these ecosystems with beneficial bacteria through fecal microbiota transplantation is thus a proposedly useful therapeutic; however, clinical success has varied, necessitating research into strategies to improve outcomes. Antibiotic pretreatment has been suggested as one such approach, but concerns over harmful side effects have hindered testing this hypothesis clinically. Here, we evaluate the use of bioreactors supporting defined microbial communities derived from human fecal samples as models of the colonic microbiota in determining the effectiveness of antibiotic pretreatment. We found that relative antimicrobial resistance was a key determinant of successful microbial engraftment with rifaximin (broad-spectrum antibiotic) pretreatment, despite careful timing of the application of the therapeutic agents, resulting in distinct species profiles from those of the control but with similar overall outcomes. Our model had results comparable to the clinical findings and thus can be used to screen for useful antibiotics.
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http://dx.doi.org/10.1128/mSystems.00404-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6989129PMC
January 2020

A survey of genes modulated by host cell infection.

Microb Genom 2020 02 29;6(2). Epub 2019 Oct 29.

Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

Here, we report comprehensive transcriptomic profiles from under conditions that mimic the first stages of bacterial infection in a highly differentiated adenocarcinoma epithelial cell line. Our transcriptomic adenocarcinoma approach allows us to measure the expression dynamics and regulation of bacterial virulence and response factors in real time, and is a novel strategy for clarifying the role of infection in colorectal cancer (CRC) progression. Our data show that: (i) infection alters metabolic and functional pathways in , allowing the bacterium to adapt to the host-imposed milieu; (ii) infection also stimulates the expression of genes required to help induce and promote a hypoxic and inflammatory microenvironment in the host; and (iii) invasion occurs by a haematogenous route of infection. Our study identifies novel gene targets from that are activated during invasion and which may aid in determining how this species invades and promotes disease within the human gastrointestinal tract. These invasion-specific genes may be useful as biomarkers for CRC progression in a host and could also assist in the development of new diagnostic tools and treatments (such as vaccines or small molecule drug targets), which will be able to combat infection and inflammation in the host while circumventing the potential problem of tolerization.
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http://dx.doi.org/10.1099/mgen.0.000300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067209PMC
February 2020

Perspectives for Consideration in the Development of Microbial Cell Reference Materials.

Cancer Epidemiol Biomarkers Prev 2019 12 12;28(12):1949-1954. Epub 2019 Sep 12.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.

Microbiome measurement and analyses benefit greatly from incorporation of reference materials as controls. However, there are many points to consider in defining an ideal whole-cell reference material standard. Such a standard would embody all the diversity and measurement challenges present in real samples, would be completely characterized to provide "ground truth" data, and would be inexpensive and widely available. This ideal is, unfortunately, not readily attainable because of the diverse nature of different sequencing projects. Some applications may benefit most from highly complex reference materials, while others will value characterization or low expense more highly. The selection of appropriate microbial whole-cell reference materials to benchmark and validate microbial measurements should be considered carefully and may vary among specific applications. In this article, we describe a perspective on the development of whole-cell microbial reference materials for use in metagenomics analyses.
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http://dx.doi.org/10.1158/1055-9965.EPI-19-0557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6891190PMC
December 2019

Drivers of human gut microbial community assembly: coadaptation, determinism and stochasticity.

ISME J 2019 12 2;13(12):3080-3092. Epub 2019 Sep 2.

Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.

Microbial community assembly is a complex process shaped by multiple factors, including habitat filtering, species assortment and stochasticity. Understanding the relative importance of these drivers would enable scientists to design strategies initiating a desired reassembly for e.g., remediating low diversity ecosystems. Here, we aimed to examine if a human fecal-derived defined microbial community cultured in bioreactors assembled deterministically or stochastically, by completing replicate experiments under two growth medium conditions characteristic of either high fiber or high protein diets. Then, we recreated this defined microbial community by matching different strains of the same species sourced from distinct human donors, in order to elucidate whether coadaptation of strains within a host influenced community dynamics. Each defined microbial ecosystem was evaluated for composition using marker gene sequencing, and for behavior using H-NMR-based metabonomics. We found that stochasticity had the largest influence on the species structure when substrate concentrations varied, whereas habitat filtering greatly impacted the metabonomic output. Evidence of coadaptation was elucidated from comparisons of the two communities; we found that the artificial community tended to exclude saccharolytic Firmicutes species and was enriched for metabolic intermediates, such as Stickland fermentation products, suggesting overall that polysaccharide utilization by Firmicutes is dependent on cooperation.
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http://dx.doi.org/10.1038/s41396-019-0498-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863822PMC
December 2019

Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health.

Microbiome 2019 06 13;7(1):91. Epub 2019 Jun 13.

Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.

The human gut microbiome is a critical component of digestion, breaking down complex carbohydrates, proteins, and to a lesser extent fats that reach the lower gastrointestinal tract. This process results in a multitude of microbial metabolites that can act both locally and systemically (after being absorbed into the bloodstream). The impact of these biochemicals on human health is complex, as both potentially beneficial and potentially toxic metabolites can be yielded from such microbial pathways, and in some cases, these effects are dependent upon the metabolite concentration or organ locality. The aim of this review is to summarize our current knowledge of how macronutrient metabolism by the gut microbiome influences human health. Metabolites to be discussed include short-chain fatty acids and alcohols (mainly yielded from monosaccharides); ammonia, branched-chain fatty acids, amines, sulfur compounds, phenols, and indoles (derived from amino acids); glycerol and choline derivatives (obtained from the breakdown of lipids); and tertiary cycling of carbon dioxide and hydrogen. Key microbial taxa and related disease states will be referred to in each case, and knowledge gaps that could contribute to our understanding of overall human wellness will be identified.
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http://dx.doi.org/10.1186/s40168-019-0704-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567490PMC
June 2019

Gut microbial biofilm composition and organisation holds the key to CRC.

Nat Rev Gastroenterol Hepatol 2019 06;16(6):329-330

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

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http://dx.doi.org/10.1038/s41575-019-0148-4DOI Listing
June 2019

Association of HLA-dependent islet autoimmunity with systemic antibody responses to intestinal commensal bacteria in children.

Sci Immunol 2019 02;4(32)

Hospital for Sick Children, Toronto, ON, Canada.

Microbiome sequence analyses have suggested that changes in gut bacterial composition are associated with autoimmune disease in humans and animal models. However, little is known of the mechanisms through which the gut microbiota influences autoimmune responses to distant tissues. Here, we evaluated systemic antibody responses against cultured human gut bacterial strains to determine whether observed patterns of anticommensal antibody (ACAb) responses are associated with type 1 diabetes (T1D) in two cohorts of pediatric study participants. In the first cohort, ACAb responses in sera collected from participants within 6 months of T1D diagnosis were compared with age-matched healthy controls and also with patients with recent onset Crohn's disease. ACAb responses against multiple bacterial species discriminated among these three groups. In the second cohort, we asked whether ACAb responses present before diagnosis were associated with later T1D development and with genotype in participants who were discordant for subsequent progression to diabetes. Serum IgG2 antibodies against and against a bacterial consortium were associated with future T1D diagnosis in an haplotype-dependent manner. These analyses reveal associations between antibody responses to intestinal microbes and genotype and islet autoantibody specificity and with a future diagnosis of T1D. Further, we present a platform to investigate antibacterial antibodies in biological fluids that is applicable to studies of autoimmune diseases and responses to therapeutic interventions.
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http://dx.doi.org/10.1126/sciimmunol.aau8125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380548PMC
February 2019

Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile.

Sci Rep 2019 01 29;9(1):885. Epub 2019 Jan 29.

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
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http://dx.doi.org/10.1038/s41598-018-37547-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351598PMC
January 2019

Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.

Front Microbiol 2018 30;9:2559. Epub 2018 Oct 30.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States.

Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as in inflammatory bowel disease (IBD) patients, is of great interest. To date, most studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of strains in a left-sided CD patient, who exhibited sustained levels of greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of strains, and found that the abundance and dominance of specific strains in the community varied over time; (2) performed strain-level assemblies of seven dominant strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of strains with specific traits. Therefore, strain-level time-series analysis of dominant strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.
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http://dx.doi.org/10.3389/fmicb.2018.02559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218438PMC
October 2018

Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.

Genome Biol Evol 2018 09 1;10(9):2255-2265. Epub 2018 Sep 1.

Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.

Homologous genes in prokaryotes can be described using phylogenetic profiles which summarize their patterns of presence or absence across a set of genomes. Phylogenetic profiles have been used for nearly twenty years to cluster genes based on measures such as the Euclidean distance between profile vectors. However, most approaches do not take into account the phylogenetic relationships amongst the profiled genomes, and overrepresentation of certain taxonomic groups (i.e., pathogenic species with many sequenced representatives) can skew the interpretation of profiles. We propose a new approach that uses a coevolutionary method defined by Pagel to account for the phylogenetic relationships amongst target organisms, and a hierarchical-clustering approach to define sets of genes with common distributions across the organisms. The clusters we obtain using our method show greater evidence of phylogenetic and functional clustering than a recently published approach based on hidden Markov models. Our clustering method identifies sets of amino-acid biosynthesis genes that constitute cohesive pathways, and motility/chemotaxis genes with common histories of descent and lateral gene transfer.
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http://dx.doi.org/10.1093/gbe/evy178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6130602PMC
September 2018

Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome.

Am J Physiol Endocrinol Metab 2018 12 21;315(6):E1087-E1097. Epub 2018 Aug 21.

National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland.

A 2-day workshop organized by the National Institutes of Health and U.S. Department of Agriculture included 16 presentations focused on the role of diet in alterations of the gastrointestinal microbiome, primarily that of the colon. Although thousands of research projects have been funded by U.S. federal agencies to study the intestinal microbiome of humans and a variety of animal models, only a minority addresses dietary effects, and a small subset is described in sufficient detail to allow reproduction of a study. Whereas there are standards being developed for many aspects of microbiome studies, such as sample collection, nucleic acid extraction, data handling, etc., none has been proposed for the dietary component; thus this workshop focused on the latter specific point. It is important to foster rigor in design and reproducibility of published studies to maintain high quality and enable designs that can be compared in systematic reviews. Speakers addressed the influence of the structure of the fermentable carbohydrate on the microbiota and the variables to consider in design of studies using animals, in vitro models, and human subjects. For all types of studies, strengths and weaknesses of various designs were highlighted, and for human studies, comparisons between controlled feeding and observational designs were discussed. Because of the lack of published, best-diet formulations for specific research questions, the main recommendation is to describe dietary ingredients and treatments in as much detail as possible to allow reproduction by other scientists.
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http://dx.doi.org/10.1152/ajpendo.00058.2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415710PMC
December 2018

Using bioreactors to study the effects of drugs on the human microbiota.

Methods 2018 10 11;149:31-41. Epub 2018 Aug 11.

Gastrointestinal Disease Research Unit, Kingston Health Sciences Center, Kingston, ON, Canada; Division of Microbiology and Infectious Diseases, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Medicine, Kingston Health Sciences Center, Kingston, ON, Canada.

The study of complex microbial communities has become a major research focus as mounting evidence suggests the pivotal role microbial communities play in host health and disease. Microbial communities of the gastrointestinal tract, known as the gut microbiota, have been implicated in aiding the host with vitamin biosynthesis, regulation of host energy metabolism, immune system development, and resistance to pathogen invasion. Conversely, disruptions of the gut microbiota have been linked to host morbidity, including the development of inflammatory diseases, metabolic disorders, increased cardiovascular risk, and increased risk of infectious diseases. However, studying the gut microbiota in humans and animals is challenging, as many microorganisms are fastidious with unique nutritional or environmental requirements that are often not met using conventional culture techniques. Bioreactors provide a unique solution to overcome some of the limitations of conventional culture techniques. Bioreactors have been used to propagate and establish complex microbial communities in vitro by recapitulating the physiological conditions found in the GI tract. These systems further our understanding of microbial physiology and facilitate our understanding of the impact of medications and xenobiotics on microbial communities. Here, we review the versatility and breadth of bioreactor systems that are currently available and how they are being used to study faecal and defined microbial communities. Bioreactors provide a unique opportunity to study complex microbial interactions and perturbations in vitro in a controlled environment without confounding biotic and abiotic variables.
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http://dx.doi.org/10.1016/j.ymeth.2018.08.003DOI Listing
October 2018

Moderate Renal Impairment and Toxic Metabolites Produced by the Intestinal Microbiome: Dietary Implications.

J Ren Nutr 2019 01 9;29(1):55-64. Epub 2018 Aug 9.

Stroke Prevention & Atherosclerosis Research Centre, Robarts Research Institute, Western University, London, Canada; Divisions of Neurology and Clinical Pharmacology, Western University, London, Canada. Electronic address:

Objective: Toxic metabolites produced by the intestinal microbiome from animal proteins, carnitine (mainly from red meat), or phosphatidylcholine (mainly from egg yolk), have important adverse effects on cardiovascular disease. These are renally eliminated and may be termed gut-derived uremic toxins (GDUT). We hypothesized that even moderate renal impairment and intake of nutrient precursors would raise plasma levels of GDUT.

Design: A cohort study.

Setting: Academic medical center.

Subjects: Patients attending stroke prevention clinics at a university medical center were recruited.

Main Outcome Measure: Nutrient intake was assessed by the 131-item Harvard Food Frequency Questionnaire; estimated glomerular filtration rate (eGFR) was caculated using the Chronic Kidney Disease-Epidemiology (EPI) equations. Plasma levels of trimethylamine n-oxide, p-cresyl sulfate, hippuric acid, p-cresyl glucuronide, pheny acetyl glutamine, and phenyl sulfate were measured by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry.

Results: Among 316 patients recruited, the mean (standard deviation [SD]) age was 66.74 (10.42) years; 59.7% were men. Mean eGFR was 76.03 ± 20.01; 57 (18%) had eGFR<60 mL/min/1.73 m. Plasma levels of all GDUT were significantly higher even with moderate reduction of eGFR. Nutrient intake affected plasma levels of some GDUT; the effects differed by eGFR above and below 60 mL/min/1.73 m. Plasma levels were obtained fasting, so we probably underestimated the effect of nutrient intake.

Conclusions: Even moderate impairment of renal function was associated with higher plasma levels of GDUT. This has dietary implications for patients at risk of atherosclerosis, particularly in those with impaired renal function (including the elderly): they should limit intake of animal protein, red meat, and egg yolk. It also points the way to novel approaches to vascular prevention, including more intensive dialysis, renal transplantation, and modification of the intestinal microbiome with probiotics or fecal transplantation.
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http://dx.doi.org/10.1053/j.jrn.2018.05.007DOI Listing
January 2019

Guelph Family Health Study: pilot study of a home-based obesity prevention intervention.

Can J Public Health 2018 08 25;109(4):549-560. Epub 2018 Apr 25.

Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Canada.

Objective: To examine the feasibility and preliminary impact of a home-based obesity prevention intervention among Canadian families.

Methods: Families with children 1.5-5 years of age were randomized to one of three groups: (1) four home visits (HV) with a health educator, emails, and mailed incentives (4HV; n = 17); (2) two HV, emails, and mailed incentives (2HV; n = 14); or (3) general health advice through emails (control; n = 13). Parents randomized to the 2HV and 4HV groups completed post-intervention satisfaction surveys. At baseline and post-intervention, parents reported frequency of family meals and their children's fruit, vegetable, and sugar-sweetened beverage (SSB) intake. We assessed the children's physical activity, sedentary behaviour, and sleep using accelerometers and their % fat mass using bioelectrical impedance analysis. Differences in outcomes at post-intervention, controlling for baseline, were examined using generalized estimating equations.

Results: Of the 44 families enrolled, 42 (96%) had 6-month outcome data. Satisfaction with the intervention was high; 80% were "very satisfied" and 20% were "satisfied." At post-intervention, children randomized to the 4HV and 2HV groups had significantly higher fruit intake and children randomized to the 2HV group had significantly lower percentage of fat mass, as compared to the control. No significant intervention effect was found for frequency of family meals, the children's vegetable or SSB intake, physical activity, sedentary behaviour, or sleep.

Conclusions: Our results suggest that the delivery of a home-based intervention is feasible among Canadian families and may lead to improved diet and weight outcomes among children. A full-scale trial is needed to test the effectiveness of this home-based intervention.

Clinical Trials Registration Number: NCT02223234.
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http://dx.doi.org/10.17269/s41997-018-0072-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964565PMC
August 2018

Mediterranean Diet Score: Associations with Metabolic Products of the Intestinal Microbiome, Carotid Plaque Burden, and Renal Function.

Nutrients 2018 Jun 16;10(6). Epub 2018 Jun 16.

Stroke Prevention & Atherosclerosis Research Centre, Robarts Research Institute, Western University, 1400 Western Road, London, ON N6G 2V4, Canada.

Metabolic products of the intestinal microbiome such as trimethylamine N-oxide (TMAO) that accumulate in renal failure (gut-derived uremic toxins, GDUTs) affect atherosclerosis and increase cardiovascular risk. We hypothesized that patients on a Mediterranean diet and those consuming lower amounts of dietary precursors would have lower levels of GDUTs. Patients attending vascular prevention clinics completed a Harvard Food Frequency Questionnaire (FFQ) and had plasma levels of TMAO, p-cresylsulfate, hippuric acid, indoxyl sulfate, p-cresyl glucuronide, phenyl acetyl glutamine, and phenyl sulfate measured by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. Carotid plaque burden was measured by ultrasound; CKD-Epi equations were used to estimate the glomerular filtration rate. In total, 276 patients completed the study. Even moderate renal function significantly increased plasma GDUTs, which were significantly associated with higher carotid plaque burden. There was no significant difference in plasma levels of any GDUT associated with a Mediterranean diet score or with intake of dietary precursors. In omnivorous patients with vascular disease, the intake of dietary precursors of intestinal metabolites or adherence to a Mediterranean diet did not change plasma GDUT. Approaches other than diet, such as probiotics and repopulation of the intestinal microbiome, may be required to mitigate the adverse effects of GDUTs.
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http://dx.doi.org/10.3390/nu10060779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024790PMC
June 2018
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