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Zachary A. Costliow

Other affiliations: Broad Institute
Bio: Zachary A. Costliow is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Bacteroides & Bacteroides thetaiotaomicron. The author has an hindex of 2, co-authored 4 publications receiving 42 citations. Previous affiliations of Zachary A. Costliow include Broad Institute.

Papers
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Journal ArticleDOI
31 Oct 2017
TL;DR: Thiamine acquisition mechanisms used by B. thetaiotaomicron not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut, adding further evidence that altering the presence or concentrations of water-soluble vitamins such as thiamines may be an effective method for manipulating gut community composition.
Abstract: Thiamine (vitamin B1) is an essential cofactor for all organisms. Humans primarily acquire thiamine through their diet, and thiamine deficiencies have adverse neurological effects. However, the role gut microbes play in modulating thiamine availability is poorly understood, and little is known about how thiamine impacts the stability of microbial gut communities. To investigate thiamine's role in the gut, we utilized the model gut microbe Bacteroides thetaiotaomicron. Transcriptome sequencing (RNA-seq) revealed a global downregulation of thiamine and amino acid biosynthesis, glycolysis, and purine metabolism when thiamine was present. Using genetic mutants with thiamine biosynthesis and transport locus mutations, we determined both systems were critical for growth in thiamine-deficient medium. The defect in the double transport mutant suggests an uncharacterized feedback mechanism between thiamine transport and biosynthesis in B. thetaiotaomicron. Mutant phenotypes were recapitulated during pairwise competitions, reinforcing the importance of encoding versatile thiamine acquisition mechanisms when thiamine concentrations are variable. In addition, liquid chromatography-mass spectrometry (LC-MS) analyses corroborate that exogenous thiamine levels affect the internal thiamine pool of B. thetaiotaomicron. Furthermore, we computationally examined the ability of other gut microbes to acquire thiamine and identified lineage-specific differences in thiamine acquisition strategies. Among the Bacteroidetes, the capacities for both thiamine transport and biosynthesis are common. Together, these data show that thiamine acquisition mechanisms used by B. thetaiotaomicron not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut. IMPORTANCE Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is expected to impact the structure and stability of the microbiota, and ultimately this variation may have both direct and indirect effects on human health. Our study identifies the diverse strategies employed by gut Bacteroidetes to acquire thiamine. We demonstrate how the presence or absence of thiamine biosynthesis or transport dramatically affects the abundance of B. thetaiotaomicron in a competitive environment. This study adds further evidence that altering the presence or concentrations of water-soluble vitamins such as thiamine may be an effective method for manipulating gut community composition. In turn, targeted thiamine delivery could be used therapeutically to alter dysbiotic communities linked to disease. Author Video: An author video summary of this article is available.

51 citations

Journal ArticleDOI
TL;DR: Xavier et al. as mentioned in this paper examined cell type-specific roles of the pH sensor G protein-coupled receptor 65 (GPR65) and its inflammatory disease-associated Ile231Leu-coding variant in inflammation control.
Abstract: Extracellular acidification occurs in inflamed tissue and the tumor microenvironment; however, a systematic study on how pH sensing contributes to tissue homeostasis is lacking. In the present study, we examine cell type-specific roles of the pH sensor G protein-coupled receptor 65 (GPR65) and its inflammatory disease-associated Ile231Leu-coding variant in inflammation control. GPR65 Ile231Leu knock-in mice are highly susceptible to both bacterial infection-induced and T cell-driven colitis. Mechanistically, GPR65 Ile231Leu elicits a cytokine imbalance through impaired helper type 17 T cell (TH17 cell) and TH22 cell differentiation and interleukin (IL)-22 production in association with altered cellular metabolism controlled through the cAMP–CREB–DGAT1 axis. In dendritic cells, GPR65 Ile231Leu elevates IL-12 and IL-23 release at acidic pH and alters endo-lysosomal fusion and degradation capacity, resulting in enhanced antigen presentation. The present study highlights GPR65 Ile231Leu as a multistep risk factor in intestinal inflammation and illuminates a mechanism by which pH sensing controls inflammatory circuits and tissue homeostasis. Extracellular microenvironments are more acidic upon tissue damage or in tumors. Xavier and colleagues identify a role for the pH-sensitive, G protein-coupled receptor GPR65 in multiple aspects of immune cell lipid metabolism, disruption of which leads to chronic inflammatory responses.

15 citations

Journal ArticleDOI
TL;DR: In this paper, a purified RNA-binding protein (RBP) from Bacteroides thetaiotaomicron was found to be able to bind to single-stranded RNA in vitro with an affinity similar to other characterized RBPs.
Abstract: Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here, we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. IMPORTANCE The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates, and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.

5 citations

Posted ContentDOI
06 Dec 2019-bioRxiv
TL;DR: The genetic basis of thiamine (Vitamin B1) uptake and biosynthesis in three representative Bacteroides species is investigated and implies that gut Bactseroides have evolved distinct strategies for making or acquiring an essential nutrient.
Abstract: Thiamine (vitamin B1) and its phosphorylated precursors are necessary for decarboxylation reactions required in carbohydrate and branched chain amino acid metabolism. Due to its critical roles in central metabolism, thiamine is essential for human and animal hosts and their resident gut microbes. However, little is known about how thiamine availability shapes the composition of gut microbial communities and the physiology of individual species within those communities. Our previous work has implicated both thiamine biosynthesis and transport activities in the fitness of Bacteroides species. To better understand thiamine-dependent gene regulation in Bacteroides, we examined thiamine biosynthesis and transport genes in three representative species: Bacteroides thetaiotaomicron, Bacteroides uniformis, and Bacteroides vulgatus. All three species possess thiamine biosynthetic operons controlled by highly conserved cis-acting thiamine pyrophosphate (TPP) riboswitches. B. thetaiotaomicron and B. uniformis have additional TPP riboswitch-controlled operons encoding thiamine transport functions. Transcriptome analyses showed that each Bacteroides species had a distinct transcriptional response to exogenous thiamine. Analysis of transcript levels and translational fusions demonstrated that in B. thetaiotaomicron, the TPP riboswitch upstream of biosynthesis genes acts at the level of transcription, while TPP riboswitches upstream of transport operons work at the level of translation. In B. uniformis and B. vulgatus, TPP riboswitches work at the transcriptional level to control downstream operons. The varying responses to exogenous thiamine and use of varied regulatory mechanisms may play an important role in niche establishment by the Bacteroidetes in the complex and constantly shifting gut environment. Importance Bacteroides species are important and abundant members of human gut microbiome communities. Their activities in the gut are influenced by constant changes in nutrient availability. In this study, we investigated the genetic basis of thiamine (Vitamin B1) uptake and biosynthesis in three representative Bacteroides species. We found species-specific differences in the response to exogenous thiamine, and distinct mechanisms for regulation of uptake and biosynthesis gene expression. Our work implies that gut Bacteroides have evolved distinct strategies for making or acquiring an essential nutrient. These mechanisms may play an important role in the success of Bacteroides in establishing a niche within complex gut microbiome communities.

5 citations

Posted ContentDOI
28 Apr 2021-bioRxiv
TL;DR: A purified RNA-binding protein (RBP) from Bacteroides thetaiotaomicron was found to have an affinity similar to other characterized regulatory RBPs.
Abstract: Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. Importance The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.

Cited by
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Journal ArticleDOI
TL;DR: It is proposed that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression because bacterial functions are conserved across taxonomic groups.
Abstract: Background: Recently discovered relationships between the gastrointestinal microbiome and the brain have implications for psychiatric disorders, including major depressive disorder (MDD). Bacterial transplantation from MDD patients to rodents produces depression-like behaviors. In humans, case-control studies have examined the gut microbiome in healthy and affected individuals. We systematically reviewed existing studies comparing gut microbial composition in MDD and healthy volunteers. Methods: A PubMed literature search combined the terms “depression,” “depressive disorder,” “stool,” “fecal,” “gut,” and “microbiome” to identify human case-control studies that investigated relationships between MDD and microbiota quantified from stool. We evaluated the resulting studies, focusing on bacterial taxa that were different between MDD and healthy controls. Results: Six eligible studies were found in which 50 taxa exhibited differences (p<0.05) between patients with MDD and controls. Patient characteristics and methodologies varied widely between studies. Five phyla—Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Protobacteria—were represented; however, divergent results occurred across studies for all phyla. The largest number of differentiating taxa were within phylum Firmicutes, in which nine families and twelve genera differentiated the diagnostic groups. The majority of these families and genera were found to be statistically different between the two groups in two studies identified. Family Lachnospiraceae differentiated the diagnostic groups in four studies (with an even split in directionality). Across all five phyla, nine genera were higher in MDD (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasuterella, Phascolarctobacterium, and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium, and Ruminococcus), and six were divergent (Alistipes, Bacteroides, Megamonas, Oscillibacter, Prevotella, and Roseburia). We highlight mechanisms and products of bacterial metabolism as they may relate to the etiology of depression. Conclusions: No consensus has emerged from existing human studies of depression and gut microbiome concerning which bacterial taxa are most relevant to depression. This may in part be due to differences in study design. Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression.

321 citations

Journal ArticleDOI
TL;DR: The composition and function of the intestinal microbiota may affect host B vitamin usage and, by extension, host immunity, and the immunological functions of B vitamins and their metabolism by intestinal bacteria with respect to the control of host immunity are reviewed.
Abstract: Vitamins are micronutrients that have physiological effects on various biological responses, including host immunity. Therefore, vitamin deficiency leads to increased risk of developing infectious, allergic, and inflammatory diseases. Since B vitamins are synthesized by plants, yeasts, and bacteria, but not by mammals, mammals must acquire B vitamins from dietary or microbial sources, such as the intestinal microbiota. Similarly, some intestinal bacteria are unable to synthesize B vitamins and must acquire them from the host diet or from other intestinal bacteria for their growth and survival. This suggests that the composition and function of the intestinal microbiota may affect host B vitamin usage and, by extension, host immunity. Here, we review the immunological functions of B vitamins and their metabolism by intestinal bacteria with respect to the control of host immunity.

288 citations

Journal ArticleDOI
TL;DR: The function of single B-vitamin in the distal gut including their roles in relation to bacteria is reviewed and the prospect of extending analytical methods to better understand the role of B- vitamins in the gut is explored.
Abstract: The gut microbiota produce hundreds of bioactive compounds, including B-vitamins, which play significant physiological roles in hosts by supporting the fitness of symbiotic species and suppressing the growth of competitive species. B-vitamins are also essential to the host and certain gut bacterium. Although dietary B-vitamins are mainly absorbed from the small intestine, excess B-vitamins unable to be absorbed in the small intestine are supplied to the distal gut. In addition, B-vitamins are supplied from biosynthesis by distal gut microbiota. B-vitamins in the distal colon may perform many important functions in the body. They act as 1) nutrients for a host and their microbiota, 2) regulators of immune cell activity, 3) mediators of drug efficacy, 4) supporters of survival, or the fitness of certain bacterium, 5) suppressors of colonization by pathogenic bacteria, and 6) modulators of colitis. Insights into basic biophysical principles, including the bioavailability of B-vitamins and their derivatives in the distal gut are still not fully elucidated. Here, the function of single B-vitamin in the distal gut including their roles in relation to bacteria are briefly reviewed. The prospect of extending analytical methods to better understand the role of B-vitamins in the gut is also explored.

65 citations

Journal ArticleDOI
TL;DR: Cross‐feeding between formate‐producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production.
Abstract: © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

48 citations

Journal ArticleDOI
TL;DR: Vitamins may play a critical role in driving microbiome dynamics and thus provide new avenues for modification of the microbiome and a functional link between TonB-dependent outer-membrane transport and PnuTbased inner-memBRane transport of thiamine is suggested.
Abstract: The mammalian gut microbiome is one of the densest known microbial communities [1]. These microbial communities are largely composed of four major phyla (Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria). Our understanding of the factors that shape gut microbial community composition is largely based on the “primary economy” of this ecosystem: the flow of carbon from the diet to bacterial biomass and fermentation products [2]. However, many enzymatic reactions in this primary economy depend on cofactors that are derived from vitamins, which are much less abundant but no less important. Vitamins may play a critical role in driving microbiome dynamics and thus provide new avenues for modification of the microbiome. Microbes require different combinations of a variety of vitamins. These include fat-soluble vitamins, such as vitamins A, D, E, and K, and water-soluble vitamins, such as vitamin C and the B vitamins. The B vitamins are a broad category of small molecules that are important for cell metabolism but otherwise do not necessarily share structural or functional characteristics. The family of B vitamins includes thiamine (B1) (Fig 1A), riboflavin (B2), niacin (B3), pantothenic acid (B5), pyridoxine (B6), biotin (B7), folate (B9), and cyanocobalamin (B12) (Fig 1C). Cyanocobalamin belongs to the cobamide family, which includes many different vitamin B12– like molecules. Thiamine and cobamide provide examples of the elaborate mechanisms gut microbes use to capture vitamins. Thiamine is required by all organisms due to its role in essential metabolic pathways, including glycolysis and the tricarboxylic acid (TCA) cycle [3]. Among gut microbes, approximately half encode the enzymes for de novo thiamine synthesis [3]. This synthesis includes production of the precursors thiazole and hydroxymethyl pyrimidine followed by the combination of these precursors into thiamine [4]. Bacteria, both within the gut and in other systems such as aquatic bacterioplankton, can acquire these precursors or mature thiamine via transport from their environment instead of or in addition to synthesis [5]. Transport of mature thiamine occurs through systems such as the ATP-binding cassette (ABC)-type transporter ThiBPQ (in Proteobacteria) and the group II energy-coupling factor (ECF) transporter ThiT (in Firmicutes) [6, 7]. Additionally, some proteins annotated as vitamin B3 transporters can transport thiamine, including NiaP and some Pnu transporters [8, 9]. Although the gut Bacteroidetes do not encode any previously characterized thiamine transporters, they do encode PnuT as a putative inner membrane transporter [3, 9]. Genes encoding PnuT can be in close proximity to genes for TonB-dependent outer-membrane transporters in Bacteroidetes, suggesting a functional link between TonB-dependent outer-membrane transport and PnuTbased inner-membrane transport of thiamine [4]. A heterologous expression system in Escherichia coli provided the first experimental support for this hypothesis [9]. Additional studies in the gut commensal Bacteroides thetaiotaomicron have shown that a TonB-dependent outer-

41 citations