Biology subjects

Krajmalnik-Brown, R.

Publications and source records attributed to Krajmalnik-Brown, R..

14 recordsLinked to original sources

bioRxiv2026

Human Gut Microbiota of Healthy Individuals Show Resilience to Acute Aflatoxin B1 Exposure Despite Solvent-Driven Community Shifts

Aflatoxin B1 (AFB1) is a potent mycotoxin linked to severe systemic health issues and gut microbiome disruption in in vivo models. However, it remains unclear whether AFB1 directly impairs human gut microbial composition and function or if observed dysbiosis is host-mediated. The objective of this work was to investigate the direct impact of acute AFB1 exposure on human gut microbiota from healthy individuals using anaerobic batch bioreactors. Fecal inoculum from 17 healthy adults was exposed to AFB1 concentrations ranging from 1,000 to 5,000 ppb, delivered in two solvents (ethanol and corn oil) under conditions simulating the large intestine. Metabolic activity was assessed via short-chain fatty acid (SCFA) and gas production measurements, while community structure was assessed using 16S rRNA gene amplicon sequencing. AFB1 concentrations remained stable throughout the incubations, indicating no significant microbial degradation of AFB1. Results showed that AFB1 did not significantly alter microbial SCFA output or community composition compared to solvent-only controls. Observed shifts in microbial profiles were primarily driven by the solvents used to bring AFB1 into solution rather than by the toxin. These findings demonstrate that healthy human gut microbial communities are resilient to direct, acute AFB1 exposure even at concentrations exceeding typical dietary levels. This suggests that microbiome disruption reported in vivo may be an indirect consequence of host-mediated factors, such as reactive metabolites or systemic immune responses, rather than direct toxicity by the parent compound.

microbiology↗

bioRxiv2026

Reconsidering the Use of Dimethyl Sulfoxide for Xenobiotic-Gut Microbiota Interaction Studies

Introduction: Gut microbiota are vulnerable to foreign chemicals (xenobiotics) including pharmaceuticals, environmental pollutants, and dietary contaminants such as aflatoxin B1 (AFB1) and fumonisin B1 (FB1). Assessing the effect of these xenobiotics in the laboratory requires their dissolution in a solvent vehicle, such as dimethyl sulfoxide (DMSO). While DMSO is typically used at low concentrations under the assumption of neutrality, its independent impact on microbial dynamics is a potential experimental confounder that has not been fully explored. Methods: Human fecal microbiota were cultivated in vitro for 16 days, supplemented with 0, 10, 100, and 1000 ppb of the tested xenobiotics (AFB1 or FB1) in 0.05% DMSO (v/v), with a DMSO-free control included for comparison. Microbial community dynamics were characterized via full-length 16S rRNA gene sequencing, and metabolic activity was assessed by measuring production of short-chain fatty acids and gases. Results: DMSO significantly altered microbial metabolism and drove the consistent enrichment of Desulfovibrio desulfuricans. This shift occurred across all AFB1 and FB1 treatment groups regardless of their concentrations, indicating that the biological impact of the DMSO vehicle overshadowed the specific effects of the xenobiotics. Discussion: These findings demonstrate that DMSO can induce significant microbial shifts independent of the xenobiotics under study, potentially confounding biological interpretations. This highlights a critical need for rigorous vehicle validation and the identification of safe thresholds for solvents used in microbiota research.

microbiology↗

bioRxiv2026

From Growth Faltering to Recovery: Gut Microbial and Body Composition Signatures of Early Childhood Malnutrition Phenotypes

BackgroundChronic malnutrition in early childhood is a multifactorial condition associated with long-term impairments, yet the physiological and gut microbial pathways underlying differential growth trajectories remain poorly understood. ObjectiveWe aimed to characterize phenotypic growth trajectories and identify the associated gut microbial and body composition signatures in infants during the first year of life. MethodsWe analyzed longitudinal data from birth to 12 months in a South African cohort (Soweto, n=45). Individual linear growth trajectories were modeled using the Jenss-Bayley equation, and children were clustered based on model parameters to identify phenotypic subgroups. Body composition (fat-free mass and fat mass) was measured via deuterium dilution at 6 and 12 months, and gut microbiome development was assessed using 16S rRNA gene amplicons at 4, 6, and 12 months. ResultsWe identified distinct phenotypic subgroups including healthy growth, catch-up growth, and growth faltering, that were obscured at the cohort level. These trajectories diverged most dynamically within the first 6 months of life. Integrated analysis revealed that in the growth faltering cluster, height-for-age and fat-free mass z-scores stabilized between 6 and 12 months, whereas fat mass z-scores (FMZ) declined. This trade-off is consistent with a catabolic state where energy reserves are prioritized for lean tissue and bone growth. Furthermore, at 6 months, the growth faltering cluster was enriched with opportunistic pathobionts (e.g., Paraclostridium). In contrast, the catch-up cluster exhibited a transient enrichment of facultative anaerobes (e.g., Enterobacter), supporting a hypothesis that these oxygen-tolerant taxa may help bridge a transitional microbial state in partially oxygenated or inflamed environments to enable physiological recovery. ConclusionsEarly childhood chronic malnutrition phenotypes in South African infants can be defined by distinct microbial and body composition signatures that diverge within six months of life. Integrated interventions should target both host anabolic state and microbiome transitions to support recovery.

microbiology↗

bioRxiv2025

Microbial Feast or Famine: dietary carbohydrate composition and gut microbiota metabolic function

Diet composition plays a major role in shaping the structure and function of the gut microbiota and influencing host health. While numerous studies have investigated the impact of macronutrient type and quantity on microbiota using in vitro systems, animal models, and human participants, most of these studies focused primarily on microbial-community composition and lacked the functional information that can be gained from transcript-level analyses. In this exploratory analysis, we use metatranscriptomic data to gain a functional perspective on how dietary composition is associated with the gut microbiota and hypothesized implications for host physiology. Data were derived from a tightly controlled, randomized cross-over feeding study conducted in a metabolic ward, where participants consumed two isocaloric and eucaloric diets differing in food processing and fiber content: A Western Diet (WD) limited in fiber, resistant starch, and whole foods and a Microbiome Enhancer Diet (MBD) composed of fiber-rich, whole foods. Our prior findings showed that a WD lead to a resource-limited microbiota enriched in mucin-degrading bacteria that resorted to metabolizing host-derived organic material, while the MBD supported a resource-replete microbiota that primarily metabolized dietary fiber. The objective of this work was to explore these findings more deeply using bioinformatic analyses of metatranscriptomic data. Our analysis showed increased transcription of fiber-degrading enzymes in the MBD and mucin-degrading enzymes in the WD. While in this analysis functional diversity of the gut microbiome was not affected, differences in resistant-starch and fiber content shifted the types of metabolic processes being actively transcribed. The MBD promoted biosynthetic and carbohydrate-fermenting pathways, while the WD was characterized by enzymes for host-glycan and protein degradation. Furthermore, the MBD-supported ecosystem benefits host health via enhanced SCFA production and reduced reliance on host glycan degradation. The WD fostered increased mucin and protein breakdown pathways that yield metabolites that may harm the gut barrier and systemic metabolism.

microbiology↗

bioRxiv2025

Multi-omics Integration of Microbiota Transplant Therapy in Children with Autism Spectrum Disorders

BackgroundMicrobiota transplant therapy (MTT) is a promising avenue for the substantial improvement of gastrointestinal and behavioral symptoms in children with autism spectrum disorder (ASD). Previous work has demonstrated that microbiome and metabolite profiles of children with ASD become more similar to those of their typically developing (TD) peers following MTT. MethodsTo enhance a systems-level understanding of MTT in ASD children that extends beyond previously reported findings, we present a multi-omics analysis of an ASD cohort spanning 10 weeks and 2 years of follow-up after completion of MTT. We applied cutting-edge multi-omics approaches, including metagenomics, fecal and plasma metabolomics, and advanced statistical methods, including multimodal machine learning, differential network analysis, and causal mediation analysis, to extensively characterize molecular and biochemical responses before and after MTT, to identify key taxonomic, functional, and metabolite signatures associated with MTT treatment and ASD symptoms. ResultsUsing a combination of cross-sectional and longitudinal statistical analyses and integrative machine learning techniques, we identified key meta-omic features associated with MTT. Integrated multi-omics analysis revealed that children with ASD transition to distinct biological states following MTT, clearly separated from their pre-treatment states and from TD children, as demonstrated by robust group separation and strong classification performance. Several biological signals associated with the modulation of the gut microbiome after MTT were identified, including an increase of butyrate producers such as Faecalibacterium prausnitzii and Butyricimonas faecalis; decreased fecal sulfated primary bile acid, chenodeoxycholic acid sulfate; decreased secondary bile acid, glycolithocholate sulfate; and increased sarcosine and iminodiacetate in plasma after 10 weeks of MTT compared to baseline. Differential network analysis revealed hub species, including Prevotella copri, Ruminococcus callidus, and GGB9633 SGB15091, as differentially connected 2 years after completion of MTT compared to baseline. Mediation analysis uncovered several key players as mediators of symptoms, including Alistipes ihumii, Ruminococceae, amino acid biosynthesis, bile acids, long-chain fatty acids, and cysteine-glutathione disulfide, among others. ConclusionsThis study provides one of the first comprehensive analyses of multi-omic features underlying host-microbiome interactions associated with MTT in children with ASD. It offers further evidence that fusing data across diverse molecular modalities at pre- and post- treatment time points can illuminate the potential of MTT in neurodevelopmental disorders. These findings could advance microbiome-based immunomodulatory therapies and multi-omics strategies to restore gut microbiota in children with ASD, while aiding in the discovery of novel biomarkers predictive of treatment response.

systems biology↗

bioRxiv2025

Faecalibacterium prausnitzii, depleted in the Parkinson's disease microbiome, improves motor deficits in α-synuclein overexpressing mice

Gut microbiome composition is altered in Parkinsons disease (PD), a neurodegenerative disorder characterized by motor dysfunction and frequently accompanied by gastrointestinal (GI) symptoms. Notably, microbial taxa with anti-inflammatory properties are consistently depleted in PD patients compared to controls. To explore whether specific gut bacteria may be disease-protective, we assembled a microbial consortium of 8 human-associated taxa that are reduced in individuals with PD across multiple cohorts and geographies. Treatment of -synuclein overexpressing (Thy1-ASO) mice, an animal model of PD, with this consortium improved motor and GI deficits. A single bacterial species from this consortium, Faecalibacterium prausnitzii, was sufficient to correct gut microbiome deviations in Thy1-ASO mice, induce anti-inflammatory immune responses, and promote protective colonic gene expression profiles. Accordingly, oral treatment with F. prausnitzii robustly ameliorated motor and GI symptoms and reduced -synuclein aggregates in the brain. These findings support the emerging hypothesis of functional contributions by the microbiome to PD and embolden development of potential probiotic therapies.

physiology↗

bioRxiv2025

A Sulfotransferase from a Gut Microbe Acts on Diverse Phenolic Sulfate Compounds, Including Acetaminophen Sulfate

Sulfonation is one of the two main phase II detoxification pathways in eukaryotes that transforms non-polar compounds into hydrophilic metabolites. Sulfotransferases catalyze these reactions by transferring a sulfo group from a donor to an acceptor molecule. Human cytosolic sulfotransferases use only 3-phosphoadenosine 5-phosphosulfate (PAPS) as a donor to sulfonate a variety of chemicals. Less understood are microbial aryl-sulfate sulfotransferases (ASSTs), which catalyze sulfo transfer reactions, without utilizing PAPS as a donor. Currently, the identity of physiological sulfo donor substrates remains unknown and sulfo acceptor substrates are underexplored. With this study, we aim to understand the potential contribution of a gut microbial enzyme to sulfonation chemistry by uncovering substrate preferences. Here, we show that a sulfotransferase (BvASST) from the prevalent gut microbe Bacteroides vulgatus (now Phocaeicola vulgatus) is a versatile catalyst that utilizes a wide range of phenolic molecules as substrates that are commonly encountered by the host. With this action, it has the ability to modulate concentrations of donor phenolic sulfates like acetaminophen sulfate, dopamine sulfate, p-coumaric acid sulfate, indoxyl sulfate, and p-cresol sulfate in vitro. Moreover, we report a large adaptability in the acceptor preferences with the evidence of sulfonation for many biologically relevant phenolic molecules including p-coumaric acid, p-cresol, dopamine, acetaminophen, tyramine, and 4-ethylphenol. These results suggest that such gut microbial enzymes may impact the detoxification of a variety of phenolic molecules in the host, which were previously thought to be solely detoxified via human sulfotransferases. However, further in vivo studies are necessary to understand potential contributions of ASSTs in host detoxification processes.

biochemistry↗

bioRxiv2025

Methanogens are associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy

Methanogens are CH4-producing, H2-oxidizing (i.e. hydrogenotrophic) archaea. Numerous studies have associated methanogens with obesity, but these results have been inconsistent. One link to host metabolism may be methanogens ability to consume H2, thus reducing H2 partial pressure and thermodynamically enhancing fermentation of sugars to short-chain fatty acids (SCFA) that the host can absorb. Because research linking methanogenesis to human metabolism is limited, our goal with this exploratory analysis was to investigate relationships between methanogens and other hydrogenotrophs, and the association of methanogens with human metabolizable energy (ME). Using results from a randomized crossover feeding study with well-characterized human participants and novel continuous methane measurements, we analyzed hydrogenotroph abundance and activity, fecal and serum SCFAs, and host ME between high and low CH4 producers. Methanogens were detected in about one-half of participants, and most were high CH4 producers. We found no evidence that methanogens consumption of H2 to produce CH4 affected other hydrogenotrophs. High CH4 producers had greater serum propionate and host ME irrespective of diet, as well as greater gene and transcript abundance of a key enzyme of the H2-consuming, propionate-producing succinate pathway. Finally, a network analysis revealed positive relationships between Methanobrevibacter smithii (the most prevalent methanogen in the human colon) and bacteria capable of degrading fiber and fermenting fiber- degradation products, thus forming a trophic chain to extract additional energy from undigested substrates. Our results show that methanogens in a microbial consortium were linked to host metabolizable energy through enhanced SCFA production and host SCFA absorption.

microbiology↗

bioRxiv2024

Reanalysis of metabolomics data reveals that microbiota transfer therapy modulates important fecal and plasma metabolite profiles in children with autism spectrum disorders

While Autism Spectrum Disorder (ASD) is diagnosed through behavioral symptoms and psychometric evaluations, it has also been associated with distinct metabolomic patterns. A previous clinical trial of Microbiota Transplant Therapy (MTT) in children with ASD and gastrointestinal (GI) issues revealed significant differences in plasma metabolomics between children with ASD and their typically developing (TD) counterparts, which diminished after MTT. The objective of this study was to reanalyze the plasma and fecal samples using updated metabolomics libraries at Metabolon together with a comprehensive panel of statistical methods to provide deeper insights into ASD-related metabolic differences and the impact of MTT. Compared with the original analysis, the updated annotation identified substantially more annotated metabolites and uncovered additional plasma and fecal metabolic changes associated with MTT. The reanalysis highlighted specific metabolites whose relative peak intensities differed between the ASD and TD groups, as well as metabolites with significant changes following MTT. Several plasma metabolites, including sarcosine, iminodiacetate, caproate, and caprylate, initially showed significant differences between the ASD and TD groups but shifted to resemble TD levels after MTT. In fecal samples, p-cresol sulfate and sphingolipids emerged as metabolites with altered intensities following MTT. Multivariate Fishers Discriminant Analysis (FDA) with leave-one-out cross-validation revealed that a set of metabolites including p-cresol sulfate, hydroxyproline, and caprylate could robustly classify the ASD and TD cohorts before treatment. However, after treatment, the same FDA model could no longer distinguish the two groups, as FDA scores became similar to those of the TD cohort. These findings improve our understanding of ASD-associated metabolic alterations and demonstrate that reanalysis of existing untargeted metabolomics datasets using updated metabolite annotation resources and complementary statistical approaches can reveal biologically relevant metabolite changes that were not detected previously. Larger studies with placebo-controlled designs are needed to validate these findings, further define the underlying biochemical pathways, and evaluate their potential for developing personalized therapeutic strategies. IMPORTANCEReanalysis of existing untargeted metabolomics datasets using updated metabolite annotation resources and complementary statistical approaches can reveal biological insights that were not apparent in earlier analyses. By leveraging updated metabolomics libraries and expanded statistical analyses, we identified additional annotated metabolites and uncovered plasma and fecal metabolic changes associated with autism spectrum disorder (ASD) and Microbiota Transplant Therapy (MTT). Several metabolites, including sarcosine, caprylate, and p-cresol sulfate, distinguished children with ASD from typically developing (TD) controls at baseline and shifted toward TD-like profiles following MTT. These findings demonstrate the value of periodically reanalyzing legacy metabolomics datasets as annotation resources improve, providing a more comprehensive understanding of disease-associated metabolic alterations and therapeutic responses.

neuroscience↗

bioRxiv2023

Bimodal distribution of Candida albicans in children with Autism linked with ASD symptoms

The gastrointestinal (GI) tract harbors an intricate and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e., mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. Our investigation aimed to elucidate the gut mycobiota in a cohort comprising 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants and autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We employed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in ASD compared to TD children. Total Candida and C. albicans demonstrated a bimodal distribution among children with ASD. Children with ASD with elevated Autism Treatment Evaluation Checklist (ATEC) scores (a more severe diagnosis) displayed an increased abundance of C. albicans and a decreased abundance of S. cerevisiae. A significant positive correlation was observed between ATEC scores and GI symptoms and between ATEC scores and C. albicans. Our findings propose that a deficit of beneficial fungi, specifically S. cerevisiae, and an overgrowth of C. albicans may worsen autism severity in children with ASD. Future work employing more advanced techniques (i.e., shotgun metagenomics) is encouraged to advance understanding of the functional role of fungi/yeast, and their interplay between GI symptoms and autism severity in children with ASD.

microbiology↗

bioRxiv2022

Geobacter sulfurreducens' unique metabolism results in cells with a high iron and lipid content

Geobacter sulfurreducens is a ubiquitous iron reducing bacterium in soils, and in engineered systems it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C,H,O,N, ash content) showed a high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with a high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 {+/-} 0.2 g/gdw) and lipids (32 {+/-} 0.5% dw/dw) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. ImportanceGeobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively breathing metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal, and as a ubiquitous iron reducer in soils around the world, G. sulfurreducens and its relatives impact the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organisms composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria -- these observations are important for future microbiologists and biotechnologists working with the organism.

microbiology↗

bioRxiv2022

Cytochrome expression shifts in Geobacter sulfurreducens to maximize energy conservation in response to changes in redox conditions

Previous studies have identified that Geobacter sulfurreducens has three different electron transfer pathways for respiration, and it switches between these pathways to adapt to the redox potential of its electron acceptor. However, only a small fraction of the electron carriers from each pathway have been identified. In this study, we combined electrochemical and gene expression data to identify electron carriers associated with each of the three pathways in the inner membrane, periplasm, outer membrane, and exterior of the cell. We demonstrate that it is not just the electron acceptor redox potential that controls pathway expression in G. sulfurreducens. Our method combining electrochemical modeling and transcriptomics could be adapted to better understand electron transport in other electroactive organisms with complex metabolisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/492868v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@7d1466org.highwire.dtl.DTLVardef@1c65ccborg.highwire.dtl.DTLVardef@1f64fd5org.highwire.dtl.DTLVardef@1f34293_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract was created with Biorender.com

microbiology↗

bioRxiv2019

Rapidly processed stool swabs approximate stool microbiota profiles

Studies of the intestinal microbiome commonly utilize stool samples to measure microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. In this study we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing, and evaluate the effects of shipping time at ambient temperatures on accuracy. Results indicate that swab samples reliably replicate stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (< 2 days), but sample quality quickly degrades after this period, accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity.

microbiology↗

bioRxiv2018

Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism

Bile acids are metabolic links between hosts and their gut microbiomes, yet little is known about the roles they play in microbe-to-microbe interactions. Here we present a study designed to investigate the effect that a common probiotic, Lactobacillus acidophilus, has on microbial interactions that lead to formation of secondary bile acids. A model microbial consortium was built from three human gut isolates, Clostridium scindens, Collinsella aerofaciens, and Blautia obeum, and cultured under different bile acid and probiotic treatments. A multi-omics platform that included mass spectrometry-based metabolomics and activity-based proteomic probes was used to produce two major results. The first, was that an uncommon secondary bile acid - ursocholate - was produced by a multi-species chemical synthesis pathway. This result highlights a new microbe-to-microbe interaction mediated by bile acids. The second finding was that the probiotic strain, L. acidophilus, quenched the observed interactions and effectively halted consortial synthesis of ursocholate. Little is known about the role that ursocholate plays in human health and development. However, we did discover that a decrease in ursocholate abundance corresponded with successful weight loss in patients after gastric bypass surgery versus those who did not lose weight after surgery. Hence, this study uncovered basic knowledge that may aid future designs of custom probiotic therapies to combat obesity.

microbiology↗