Discovery of bioactive microbial gene products in inflammatory bowel disease.

Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.

Complementary feeding practices of caregivers of infants with Down syndrome as compared to caregivers of typically developing infants.

Caregiver feeding practices during the complementary feeding period (6 months-2 years) may be particularly important for infants with Down syndrome (DS) as they are at higher risk for later health conditions (e.g., obesity, diabetes) that can be influenced by early feeding practices. However, how well caregivers of infants with DS are meeting infant feeding evidence-based practices is relatively unknown. Caregivers of infants with DS (N = 75) and caregivers of typically developing (TD) infants (N = 66) aged 0-2 years completed an online survey about their infant feeding practices and information sources. Caregiver practices and information sources were statistically compared between groups. Results indicated that there are significant differences in the feeding practices of caregivers of infants with DS when compared to caregivers of TD infants. Caregivers of infants with DS were less likely to meet infant feeding evidence-based practices than caregivers of TD infants. Caregivers of infants with DS were also more concerned about their infant's food intake and later weight status. Some individual feeding practices also significantly differed between groups, with caregivers of infants with DS more likely to meet evidence-based practices of purchasing iron rich foods and avoiding added salt, but less likely to use responsive feeding practices than caregivers of TD infants. Caregivers of infants with DS were also less likely to receive information about how to navigate the complementary feeding period than caregivers of TD infants. Coupled with existing research, the results of the present study suggest that infant feeding evidence-based practices should be reviewed for their appropriateness for this population and additional support for caregivers of infants with DS should be implemented to help them navigate this important period.

Preparedness of Speech Language Pathologists and Occupational Therapists to Treat Pediatric Feeding Disorder: A Cross-Sectional Survey.

BACKGROUND: Pediatric feeding disorder (PFD) is increasingly common and is often treated by speech language pathologists (SLPs) and occupational therapists (OTs) in the community setting. However, the preparedness of these disciplines to effectively address PFD is relatively unknown. METHODS: A national (US), online survey was disseminated to providers who assess and treat PFD. For the present analysis, the responses of SLPs (N = 418) and OTs (N = 195) related to their clinical background, educational background, post-graduate training, and self-rated clinical effectiveness were statistically analyzed and compared across the two disciplines. RESULTS: Both SLPs and OTs report feeling underprepared to work with PFD clients immediately following their academic training, but time spent in post-graduate training and years of clinical practice both significantly (p < 0.0001) increased feelings of effectiveness in assessing and treating PFD. Most SLPs and OTs pursued self-directed learning activities to increase competence, with the most common activities being article review, podcasts, and peer case review, although SLPs were significantly more likely to use podcasts (p < 0.0001) and peer review (p = 0.0004) than OTs. The most common barriers for providers were financial, time, travel, and institutional support barriers. CONCLUSIONS: While PFD is a key practice area of both SLPs and OTs, both provider groups feel unprepared and under-supported in providing competent care to these patients upon graduation. Future research and policy should support advancements in training for current SLPs and OTs related to PFD and address current barriers to a specialized educational pathway.

An observational study of parental language during play and mealtime in toddlers at variable likelihood for autism.

Parental language input influences child language outcomes but may vary based on certain characteristics. This research examined how parental language differs during two contexts for toddlers at varying likelihood of autism based on their developmental skills. Parental language (quantity, quality, and pragmatic functions) was analyzed during dyadic play and mealtime interactions as a secondary data analysis of observational data from a study of toddlers at elevated and lower likelihood of autism. Child developmental skills and sensory processing were also assessed. Parents used more words per minute, directives, and verbs during play and more adjectives, descriptions, and questions during mealtime. Parental language differed based on child fine motor skills, receptive language, and levels of sensory hyporesponsiveness but not autism likelihood. Overall, this study found that parental language varies based on context and child developmental skills. Future research examining parental language should include pragmatic functions and context across developmental trajectories.

Parental Decision-Making Around Introducing Complementary Foods: An Integrative Review.

A primary role in infant parenting is feeding, and this role undergoes a significant transition when introducing complementary foods (CF), with important long-term health implications. Understanding the influences on parental decision-making around timing the introduction to CF can help health care providers provide parents with effective support for feeding; however, the factors that influence parental decision-making have not been recently reviewed in the United States. To determine influences and information sources, this integrative review examined the literature from 2012 to 2022. Results indicated that parents are confused and distrustful of inconsistent and changing guidelines around CF introduction. Instead, developmental readiness signs may be a more appropriate way for practitioners and researchers to support parents in appropriate CF introduction. Future work is needed to evaluate interpersonal and societal influences on parental decision-making, as well as to develop culturally sensitive practices to support healthful parental decisions.

Statistical approaches for differential expression analysis in metatranscriptomics.

MOTIVATION: Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages) and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX. RESULTS: We designed and assessed six statistical models for DE discovery in MTX that incorporate different combinations of DNA and RNA normalization and assumptions about the underlying changes of gene copies or species abundance within communities. We evaluated these models on multiple simulated and real multi-omic datasets. Models adjusting transcripts relative to their encoding gene copies as a covariate were significantly more accurate in identifying DE from MTX in both simulated and real datasets. Moreover, we show that when paired DNA measurements (metagenomic data) are not available, models normalizing MTX measurements within-species while also adjusting for total-species RNA balance sensitivity, specificity and interpretability of DE detection, as does filtering likely technical zeros. The efficiency and accuracy of these models pave the way for more effective MTX-based DE discovery in microbial communities. AVAILABILITY AND IMPLEMENTATION: The analysis code and synthetic datasets used in this evaluation are available online at http://huttenhower.sph.harvard.edu/mtx2021. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hypocalcemia as a predictor of mortality and transfusion. A scoping review of hypocalcemia in trauma and hemostatic resuscitation.

BACKGROUND: Calcium plays an essential role in physiologic processes, including trauma's "Lethal Diamond." Thus, inadequate serum calcium in trauma patients exacerbates the effects of hemorrhagic shock secondary to traumatic injury and subsequently poorer outcomes compared to those with adequate calcium levels. Evidence to date supports the consideration of calcium derangements when assessing the risk of mortality and the need for blood product transfusion in trauma patients. This review aims to further elucidate the predictive strength of this association for future treatment guidelines and clinical trials. METHODS: Publications were collected on the relationship between i-Ca and the outcomes of traumatic injuries from PubMed, Web of Science, and CINAHL. Manuscripts were reviewed to select for English language studies. Hypocalcemia was defined as i-Ca <1.2 mmol/L. RESULTS: Using PRISMA guidelines, we reviewed 300 studies, 7 of which met our inclusion criteria. Five papers showed an association between hypocalcemia and mortality. CONCLUSIONS: In adult trauma patients, there has been an association seen between hypocalcemia, mortality, and the need for increased blood product transfusions. It is possible we are now seeing an association between low calcium levels prior to blood product administration and an increased risk for mortality and need for transfusion. Hypocalcemia may serve as a biomarker to show these needs. Therefore, hypocalcemia could potentially be used as an independent predictor for multiple transfusions such that ionized calcium measurements could be used predictively, allowing faster administration of blood products.

Multivariable association discovery in population-scale meta-omics studies.

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses generalized linear and mixed models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g., counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2's linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel diseases (IBD) across multiple time points and omics profiles.

Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome.

Emerging experimental evidence indicates that toxicant-induced alterations in gut microbiota composition and activity may affect host homeostasis. However, data from human studies are scarce; to our knowledge, no previous studies have quantified the association of lifetime exposure to environmental chemicals, across multiple time points, with the composition of the adult gut microbiome. Here we studied 124 individuals born in the Faroe Islands in 1986-1987 who were followed approximately every seven years from birth through age 28 years. Organochlorine compounds, including polychlorinated biphenyls (PCBs) and pesticides, perfluoroalkyl substances (PFAS), and mercury (Hg), were measured in cord blood and longitudinally in participants' blood. At age 28, the gut microbiome was assessed using shotgun metagenomic sequencing. Historical contaminant exposures had little direct effect on the adult gut microbiome, while a small number of fastidious anaerobes were weakly linked to recent PFAS/PFOS exposures at age 28. In this cohort, our findings suggest no lasting effects of early life exposures on adult gut microbial composition, but proximal exposures may contribute to gut microbiome alterations. The methods developed and used for this investigation may help in future identification of small but lasting impacts of environmental toxicant exposure on the gut microbiome.

Trophic-Level Interactive Effects of Phosphorus Availability on the Toxicities of Cadmium, Arsenic, and Their Binary Mixture in Media-Exposed Scenedesmus acutus and Media and Dietary-Exposed Daphnia pulex.

Various anthropogenic activities simultaneously alter essential mineral nutrients and contaminant content in the environment. Depending on essential nutrient conditions, the uptake and effects of contaminants in exposed organisms may be altered. The addressing of ecological risk assessment (ERA) of contaminant mixtures has proven difficult. Furthermore, most assessments involving single contaminant exposures do not consider the interaction of essential nutrients on toxicological end points. Hypotheses for toxicological effects of cadmium (Cd), arsenic (As), and their binary mixture (Cd/Asmix) include alteration under varying dietary and media phosphorus (P) conditions. However, interactive effects and effect size (η2) are largely unknown. Here, we investigated the toxicities of Cd-, As-, and Cd/Asmix-treated media and diets on Scenedesmus acutus (a primary producer) and Daphnia pulex (a primary consumer), under varied media and dietary P conditions [low (LP), median (MP), and optimum (COMBO)]. Our results showed significant (p < 0.05) interactive effects and concentration dependent growth inhibition of S. acutus. The toxicity (at day 7) of Cd against S. acutus was 2×, 11×, and 4× that of As in LP, MP, and COMBO conditions, respectively, while the joint toxicity effects of Cd/Asmix were partially additive in LP and COMBO, and synergistic in MP media. Furthermore, acute lethal toxicity (96 h) of Cd in D. pulex was ∼60× that of As, while Cd/Asmix joint toxicity was synergistic. Chronic toxicity (14 d) in D. pulex showed significant (p < 0.05) interaction of As and P-availability on survival, reproduction, and behavior (distance moved, velocity, acceleration and mobility), while Cd and P availability showed significant interactive effect on rotational behavior. Dose response effects of Cd, As, and Cd/Asmix in S. acutus and D. pulex were either monophasic or biphasic under varying nutrient conditions. This study provides empirical evidence of the interactive effects of media/dietary P and toxic metals (Cd, As, and Cd/Asmix) at environmentally relevant concentrations, emphasizing the need for consideration of such interactions during ERA.

Delayed inhibition of VEGF signaling after stroke attenuates blood-brain barrier breakdown and improves functional recovery in a comorbidity-dependent manner.

Diabetes is a common comorbidity in stroke patients and a strong predictor of poor functional outcome. To provide a more mechanistic understanding of this clinically relevant problem, we focused on how diabetes affects blood-brain barrier (BBB) function after stroke. Because the BBB can be compromised for days after stroke and thus further exacerbate ischemic injury, manipulating its function presents a unique opportunity for enhancing stroke recovery long after the window for thrombolytics has passed. Using a mouse model of Type 1 diabetes, we discovered that ischemic stroke leads to an abnormal and persistent increase in vascular endothelial growth factor receptor 2 (VEGF-R2) expression in peri-infarct vascular networks. Correlating with this, BBB permeability was markedly increased in diabetic mice, which could not be prevented with insulin treatment after stroke. Imaging of capillary ultrastructure revealed that BBB permeability was associated with an increase in endothelial transcytosis rather than a loss of tight junctions. Pharmacological inhibition (initiated 2.5 d after stroke) or vascular-specific knockdown of VEGF-R2 after stroke attenuated BBB permeability, loss of synaptic structure in peri-infarct regions, and improved recovery of forepaw function. However, the beneficial effects of VEGF-R2 inhibition on stroke recovery were restricted to diabetic mice and appeared to worsen BBB permeability in nondiabetic mice. Collectively, these results suggest that aberrant VEGF signaling and BBB dysfunction after stroke plays a crucial role in limiting functional recovery in an experimental model of diabetes. Furthermore, our data highlight the need to develop more personalized stroke treatments for a heterogeneous clinical population.

A pilot study: the role of the autonomic nervous system in cardiorespiratory regulation in infant feeding.

AIM: The purpose of this pilot study was to examine the interplay between the parasympathetic (PNS) and sympathetic nervous systems' (SNS) contributions to prefeeding, feeding and satiation in young, healthy infants. METHOD: This prospective study was completed on eleven full-term infants, less than 6 months old. Respiratory rate, heart rate, heart rate variability (HRV), electrodermal activity and low-frequency/high-frequency heart rate variability ratio were sampled from the infant during prefeeding, feeding and satiation periods. RESULTS: A repeated-measures ANOVA revealed a significant difference in respiratory patterning during the three feeding phases (p = .049); however, none of the other physiological measures reached significance. An emerging trend across physiological measures suggests that the feeding phase was influenced by the SNS with increasing respiratory rate, heart rate, low-frequency HRV, electrodermal activity and decreasing high-frequency HRV compared to the prefeeding and satiation phases, which were influenced predominantly by the PNS. CONCLUSION: Respiration rate increased significantly during the feeding phase compared to prefeeding and postfeeding phases. Emerging trends indicate a pattern of alternating relative tone in PNS versus SNS across feeding phases - with SNS predominating the feeding phase. More clinical research examining the SNS and PNS contributions to feeding should be completed across patient populations.

Environmental Scan of Online Government Complementary Feeding Resources in the United States.

BACKGROUND: Parents commonly seek online sources of information on the important complementary feeding period, but the accuracy of these sources varies. The 21st Century Integrated Digital Experience Act (IDEA) states federal government resources should be accurate and user-friendly; however, the quantity, quality, and accuracy of federal resources on complementary feeding is unknown. METHODS: An environmental scan of online federal, parent-facing resources about complementary feeding was conducted. The authors reviewed federal resources for concordance of information with the Dietary Guidelines for Americans (DGA). Quality was evaluated using the Patient Education Materials Assessment Tool. RESULTS: A total of 112 resources across 2 federal government departments. Overall quality was high as was concordance with recommendations from the DGA for age of complementary food introduction, foods to introduce, and foods to avoid. Allergenic food introduction and textured food progression recommendations were less consistent. Recommendations for improvements to federal resources are made. CLINICAL IMPLICATIONS: This environmental scan only included federal resources for CF. Parents may be accessing other, non-federal resources online. However, given the enactment of IDEA, it is expected that these federal resources will be up-to-date and user-friendly, which was not always the case. Nurses should review the DGA guidelines for complementary feeding and provide evidence-based anticipatory guidance to families, focusing especially on allergenic food introduction and textured food progression. Future complementary feeding interventions may benefit from directing families to online exemplars from federal sources.

The interaction between social determinants of health, health behaviors, and child's intellectual developmental diagnosis.

INTRODUCTION: Social determinants of health (SDOH) may impact caregivers' ability to implement evidence-based health practices at home during early childhood, especially in families with children with intellectual and developmental disabilities (IDD). Therefore, we examined the influence of SDOH and children's diagnosis (typically developing [TD], Down syndrome [DS], autism) on caregiver's self-report of meeting evidence-based health practices. METHODS: Caregivers (n=172) of children ages 2-6 years (TD: n=93, DS: n=40, autism: n=39) completed an online survey on SDOH and health practices related to child nutrition (CN), physical activity (PA), outdoor play (OP), and screen time (ST). A total SDOH score was computed by assigning 1 point for each favorable SDOH metric (range 0-13). Linear regressions were used to examine associations between SDOH and CN, PA, OP, ST health practices and the moderating effect of IDD diagnosis. RESULTS: Most caregivers were non-Hispanic White (84.3%), female (76.7%), 18-35 years old (55.2%), and married (89.5%). The DS group had the lowest SDOH score (mean = 8.4±1.0) compared to autism (mean = 10.1±1.0) and TD (mean = 11.0±0.9). No family scored 100% in evidence-based practices for any health practice. SDOH score was significantly associated with evidence-based practices met score for CN (b = 1.94, 95% CI = 0.84, 3.04; p = 0.001) and PA (b = 4.86, 95% CI = 2.92, 6.79; p <0.0001). Moderation analysis showed no association in the DS and autism groups between SDOH score and CN percent total score, or between SDOH score and CN, PA, and OP for percent evidence-based practices met. SDOH score was also not associated with OP percent total score for the DS group. CONCLUSIONS: This study highlights the differential influence of SDOH on caregivers' implementing health practices in families with children of different IDD diagnoses. Future research is needed to understand impacts of SDOH on non-typically developing children.

Elevated type-17 cytokines are present in axial spondyloarthritis stool.

Axial spondyloarthritis (axSpA) is characterized by type-17 immune-driven joint inflammation, and intestinal inflammation is present in around 70% of patients. In this study, we asked whether axSpA stool contained Th17-associated cytokines and whether this related to systemic Th17 activation. We measured stool cytokine and calprotectin levels by ELISA and found that patients with axSpA have increased stool IL-17A, IL-23, GM-CSF, and calprotectin. We further identified increased levels of circulating IL-17A+ and IL-17F+ T-helper cell lymphocytes in patients with axSpA compared to healthy donors. We finally assessed stool metabolites by unbiased nuclear magnetic resonance spectroscopy and found that multiple stool amino acids were negatively correlated with stool IL-23 concentrations. These data provide evidence of type-17 immunity in the intestinal lumen, and suggest its association with microbial metabolism in the intestine.

Short report: The role of oral hypersensitivity in feeding behaviors of young autistic children.

LAY ABSTRACT: Feeding problems are common among autistic children and are linked to negative health consequences. Therefore, understanding feeding problems and factors that influence these behaviors is important for developing supports for children and families. While certain sensory processing patterns are commonly associated with feeding problems, less is known about the link between sensory processing and feeding behaviors in autism, as well as how parent behaviors and feelings during mealtime differ based on child sensory preferences. This research examined two groups of young autistic children who were reported to be picky eaters by their parents: those with and those without oral hypersensitivity. Children with oral hypersensitivity had more difficulty with food acceptance and their parents reported more negative feelings around feeding their child. However, the two groups of children (oral hypersensitive and not) did not differ in their medical/oral motor symptoms, mealtime behavior, or parent use of strategies at mealtimes. This research supports the need for personalized treatment strategies based on the child's sensory preferences to support both the child and parent in managing mealtimes.

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities.

BACKGROUND: Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active ("viable") community members. Current sequence-based technologies can rarely differentiate microbial activity, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the active components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for activity assessment in synthetic and environmentally sourced microbial communities. RESULTS: In synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the active compositions of the communities. However, in the realistic environmental samples, no significant compositional differences were observed in RNA ("actively transcribed - active") vs. DNA ("whole" communities) spiked with E. coli controls, suggesting that this methodology is not appropriate for activity assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e., specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins. CONCLUSIONS: This study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent "relative" viability in realistic communities.  Video Abstract.

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.

Metagenomic assessment of gut microbial communities and risk of severe COVID-19.

BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. METHODS: We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.

Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.

Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.