Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains in vitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.

4′-Phosphopantetheinyl transferases (PPTase) post-translationally modify carrier proteins with a phosphopantetheine moiety, an essential reaction in all three domains of life. In the bacterial genus Mycobacteria, the Sfp-type PPTase activates pathways necessary for the biosynthesis of cell wall components and small molecule virulence factors. We solved the X-ray crystal structures and biochemically characterized the Sfp-type PPTases from two of the most prevalent Mycobacterial pathogens, PptT of M. tuberculosis and MuPPT of M. ulcerans. Structural analyses reveal significant differences in cofactor binding and active site composition when compared to previously characterized Sfp-type PPTases. Functional analyses including the efficacy of Sfp-type PPTase-specific inhibitors also suggest that the Mycobacterial Sfp-type PPTases can serve as therapeutic targets against Mycobacterial infections.

Diseases are often diagnosed once overt symptoms arise, ignoring the prior latent period when effective prevention may be possible. Experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis, exhibits such disease latency, but the molecular processes underlying this asymptomatic period remain poorly characterized. Gut microbes also influence EAE severity, yet their impact on the latent period remains unknown. Here, we show the latent period between immunization and EAE’s overt symptom onset is characterized by distinct host responses as measured by stool proteomics. In particular, we found a transient increase in protease inhibitors that inversely correlated with disease severity. Vancomycin administration attenuated both EAE symptoms and protease inhibitor induction potentially by decreasing immune system reactivity, supporting a subset of the microbiota’s role in modulating the host’s latent period response. These results strengthen previous evidence of proteases and their inhibitors in EAE and highlight the utility stool-omics for revealing complex, dynamic biology.

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265 words) 25 Measuring host proteins through noninvasive stool-based assays opens new avenues 26 for characterizing states of gastrointestinal health. However, the extent to which these 27 proteins vary over time and between healthy subjects is poorly characterized. Here, we 28 characterize technical and biological sources of variability in mass spectrometry-based 29 measurements of host proteins in stool. We identify the proteins that most vary over 30 time within an individual, and among different individuals. Finally, we examine and 31 compare temporal and inter-individual variation in host protein and bacterial taxonomic 32 profiles of the same fecal specimens. To address these issues, five self-reported 33 healthy individuals were each sampled eight times over four weeks. First, we 34 demonstrate that mass spectrometry-based identification and label-free quantification of 35 stool proteins exhibit non-significant variability (p>0.05) between both technical and 36 preparative replicates for a subset of 78 proteins, supporting the utility of this method for 37 biomarker measurement. Second, although 13 human stool proteins varied significantly 38 in relative abundance over time within individuals, 58 proteins varied significantly (at 39 least four-fold) between subjects. The average pair-wise difference between individuals 40 was greater than the average within-subject difference for both the proteome and 41 microbiome datasets (p<0.0001). Fecal host proteins, like the traditional fecal protein 42 marker, calprotectin, unambiguously pointed to innate and adaptive immune responses. 43For example, one subject's fecal protein profile suggested a sub-clinical inflammatory 44 state. From these data, we conclude that host-centric protein measurements in stool 45 reveal a wide range of variation during states of apparent health, and add a valuable 46 complementary insight into host-microbiota relationships. 47 IMPORTANCE 48Human proteins in stool hold untapped potential for characterizing gastrointestinal 49 health. To fully harness this potential and create a baseline of healthy stool protein 50 abundances and identifications, it will be important to establish the extent to which these 51 proteins might vary in the absence of disease. This study quantifies the major sources 52 of variation in stool protein abundance data. We assessed technical, preparative, 53 temporal, and inter-subject variability of human protein abundances in stool and found 54 3 that among these sources, differences between subjects accounted for the greatest 55 amount of variation, followed by temporal differences, and then technical factors. Our 56 paired microbiome analysis found matching patterns of temporal and inter-subject 57 variability. By characterizing multiple variance parameters in host stool protein 58 abundances, our analysis helps to contextualize a wide range of future disease-focused 59 stool studies as well as elucidate host-microbe interactions. 60 61 4 1. Introduction 62The expression of host proteins in the human ga...

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Background Inflammatory bowel disease (IBD) is a multifactorial disorder characterized by chronic gastrointestinal (GI) inflammation. In clinical practice, physicians urgently need biomarkers to monitor changes in mucosal disease to manage treatment. Non-invasive tools such as fecal biomarkers could allow for frequent monitoring of mucosal disease activity and may reflect inflammation of the entire GI tract. Towards identification of novel non-invasive fecal biomarkers, we performed a comprehensive, unbiased, analysis of the human fecal proteome from ulcerative colitis (UC), Crohn’s disease (CD) patients, and healthy controls (HC), focusing on human secreted proteins using proteomic approaches. Methods Fecal extraction processes optimized for recovery of secreted proteins were applied to stool samples of mild to severe UC and CD patients and HCs, 20 samples per group. An unbiased survey of the human fecal proteome of the IBD and HC stool extracts was performed using both data-dependent acquisition and data-independent acquisition methods on QExactive HF and Fusion Lumos mass spectrometers. Data were analyzed in Spectronaut for peptide identification, followed by analysis in MS Stats for protein quantification. Fecal calprotectin (fCAL) levels were measured in these stool samples using the Buhlmann EK-CAL immunoassay kit to correlate fCAL levels to proteomic calprotectin (S100A8/S100A9 heterodimer). Results We identified and quantified 594 differentially expressed proteins in stool using proteomics, including known proteins perturbed in IBD pathobiology. Elevated levels of neutrophilic proteins, e.g. fCal, neutrophil elastase, lactoferrin and leucine-rich Α-2 glycoprotein 1 were detected as well as proteins linked to rectal bleeding and ulceration e.g. hemoglobin subunit alpha 1 and beta. Pancreatic enzymes, suggested to be associated with active disease, were also detected. Overall, UC and CD contained many proteins not detected in HC. Differential abundances were observed between UC and CD patients, possibly reflecting differences in mucosal pathophysiology. The abundance of proteomic calprotectin correlated highly with the fCAL levels as determined by immunoassay (Spearman rank order &gt; 0.9 for S100A8 and S100A9 to fCAL), validating the fecal proteomic approach to uncover known and novel proteins of IBD biology. Conclusion We developed and qualified methods to perform fecal proteomics on IBD stool samples, enabling identification of known and novel proteins of mucosal UC and CD disease biology. In depth analysis of these proteomic datasets may reveal novel fecal biomarker candidates, targeted to reflect mucosal disease activity and potentially serve as non-invasive surrogates for endoscopy and help guide treatment in IBD patients.