scholarly journals Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe

Cell Reports ◽  
2021 ◽  
Vol 37 (13) ◽  
pp. 110164
Author(s):  
Katie A. Frye ◽  
Varadh Piamthai ◽  
Ansel Hsiao ◽  
Patrick H. Degnan
Keyword(s):  
Vitamin B12 ◽  
Competitive Dynamics ◽  
Human Gut ◽  
Gut Microbe

scholarly journals Kin selection explains the evolution of cooperation in the gut microbiota

2021 ◽  
Vol 118 (6) ◽  
pp. e2016046118 ◽  
Author(s):  
Camille Simonet ◽  
Luke McNally
Keyword(s):  
Gut Microbiota ◽  
Predictive Power ◽  
Inclusive Fitness ◽  
Evolution Of Cooperation ◽  
Community Management ◽  
Human Gut ◽  
Full Diversity ◽  
Gut Microbe ◽  
Disease Understanding ◽  
Key Parameter

Through the secretion of “public goods” molecules, microbes cooperatively exploit their habitat. This is known as a major driver of the functioning of microbial communities, including in human disease. Understanding why microbial species cooperate is therefore crucial to achieve successful microbial community management, such as microbiome manipulation. A leading explanation is that of Hamilton’s inclusive-fitness framework. A cooperator can indirectly transmit its genes by helping the reproduction of an individual carrying similar genes. Therefore, all else being equal, as relatedness among individuals increases, so should cooperation. However, the predictive power of relatedness, particularly in microbes, is surrounded by controversy. Using phylogenetic comparative analyses across the full diversity of the human gut microbiota and six forms of cooperation, we find that relatedness is predictive of the cooperative gene content evolution in gut-microbe genomes. Hence, relatedness is predictive of cooperation over broad microbial taxonomic levels that encompass variation in other life-history and ecology details. This supports the generality of Hamilton’s central insights and the relevance of relatedness as a key parameter of interest to advance microbial predictive and engineering science.

scholarly journals Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide

2019 ◽  
Vol 116 (26) ◽  
pp. 12672-12677 ◽  
Author(s):  
Matthew T. Henke ◽  
Douglas J. Kenny ◽  
Chelsi D. Cassilly ◽  
Hera Vlamakis ◽  
Ramnik J. Xavier ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Biosynthetic Gene Cluster ◽  
Spectroscopic Studies ◽  
Major Type ◽  
Human Gut ◽  
Toll Like Receptor 4 ◽  
Gut Microbe ◽  
Research Goal ◽  
Inflammatory Bowel

A substantial and increasing number of human diseases are associated with changes in the gut microbiota, and discovering the molecules and mechanisms underlying these associations represents a major research goal. Multiple studies associateRuminococcus gnavus, a prevalent gut microbe, with Crohn’s disease, a major type of inflammatory bowel disease. We have found thatR. gnavussynthesizes and secretes a complex glucorhamnan polysaccharide with a rhamnose backbone and glucose sidechains. Chemical and spectroscopic studies indicated that the glucorhamnan was largely a repeating unit of five sugars with a linear backbone formed from three rhamnose units and a short sidechain composed of two glucose units. The rhamnose backbone is made from 1,2- and 1,3-linked rhamnose units, and the sidechain has a terminal glucose linked to a 1,6-glucose. This glucorhamnan potently induces inflammatory cytokine (TNFα) secretion by dendritic cells, and TNFα secretion is dependent on toll-like receptor 4 (TLR4). We also identify a putative biosynthetic gene cluster for this molecule, which has the four biosynthetic genes needed to convert glucose to rhamnose and the five glycosyl transferases needed to build the repeating pentasaccharide unit of the inflammatory glucorhamnan.

scholarly journals Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe

Cell Reports ◽  
2020 ◽  
Vol 32 (11) ◽  
pp. 108142
Author(s):  
Danielle E. Campbell ◽  
Lindsey K. Ly ◽  
Jason M. Ridlon ◽  
Ansel Hsiao ◽  
Rachel J. Whitaker ◽  
...  
Keyword(s):  
Bile Acid ◽  
Acid Metabolism ◽  
Bile Acid Metabolism ◽  
Human Gut ◽  
Gut Microbe

scholarly journals The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29

2018 ◽  
Vol 293 (46) ◽  
pp. 17906-17916 ◽  
Author(s):  
Didier Ndeh ◽  
Jose Munoz Munoz ◽  
Alan Cartmell ◽  
David Bulmer ◽  
Corinne Wills ◽  
...  
Keyword(s):  
Dermatan Sulfate ◽  
Microbial Interactions ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Polysaccharide Lyase ◽  
Founding Member ◽  
Degrading Enzymes ◽  
Biochemical Assays ◽  
Gut Microbe ◽  
Inducible Genes

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries. The former are also an important nutrient source for select species of the human gut microbiota (HGM), a key player in host–microbial interactions. How GAGs are metabolized by the HGM is therefore of interest and has been extensively investigated in the model human gut microbe Bacteroides thetaiotaomicron. The presence of as-yet uncharacterized GAG-inducible genes in its genome and of related species, however, is testament to our incomplete understanding of this process. Nevertheless, it presents a potential opportunity for the discovery of additional GAG-degrading enzymes. Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron. NMR and UV spectroscopic assays revealed that it encodes a novel polysaccharide lyase (PL), hereafter referred to as BtCDH, reflecting its source (B. thetaiotaomicron (Bt)) and its ability to degrade the GAGs CS, dermatan sulfate (DS), and hyaluronic acid (HA). When incubated with HA, BtCDH generated a series of unsaturated HA sugars, including Δ4,5UA-GlcNAc, Δ4,5UA-GlcNAc-GlcA-GlcNac, Δ4,5UA-[GlcNAc-GlcA]2-GlcNac, and Δ4,5UA-[GlcNAc-GlcA]3-GlcNac, as end products and hence was classed as endo-acting. A combination of genetic and biochemical assays revealed that BtCDH localizes to the cell surface of B. thetaiotaomicron where it enables extracellular GAG degradation. BtCDH homologs were also detected in several other HGM species, and we therefore propose that it represents the founding member of a new polysaccharide lyase family (PL29). The current discovery also contributes new insights into CS metabolism by the HGM.

scholarly journals Gut Microbiota Metabolism and Interaction with Food Components

2020 ◽  
Vol 21 (10) ◽  
pp. 3688 ◽  
Author(s):  
Pamela Vernocchi ◽  
Federica Del Chierico ◽  
Lorenza Putignani
Keyword(s):  
Gut Microbiota ◽  
Disease Onset ◽  
Human Gut ◽  
Food Components ◽  
Host Health ◽  
Wide Variability ◽  
Gut Microbe ◽  
A Cell ◽  
Health And Disease ◽  
Biochemical Mechanisms

The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.

scholarly journals Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron

2020 ◽  
Vol 295 (52) ◽  
pp. 18625-18637
Author(s):  
Cheng-Jie Duan ◽  
Arnaud Baslé ◽  
Marcelo Visona Liberato ◽  
Joseph Gray ◽  
Sergey A. Nepogodiev ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Critical Role ◽  
Pectin Methylesterase ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
New Family ◽  
Gut Microbe ◽  
Dietary Nutrient ◽  
Helical Proteins

Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II–derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT1017oligoB using a combination of enzymatic, mass spectrometric, and NMR approaches revealed that it is a bimethylated nonaoligosaccharide (GlcA-β1,4-(2-O-Me-Xyl-α1,3)-Fuc-α1,4-(GalA-β1,3)-Rha-α1,3-Api-β1,2-(Araf-α1,3)-(GalA-α1,4)-GalA) containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an α/β-hydrolase fold, consisting of a central twisted 10-stranded β-sheet sandwiched by several α-helices. This constitutes a new fold for pectin methylesterases, which are predominantly right-handed β-helical proteins. Bioinformatic analyses revealed that the family is dominated by sequences from prominent genera of the human gut microbiota, including Bacteroides and Prevotella. Our re-sults not only highlight the critical role played by this family of enzymes in pectin metabolism but also provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.

scholarly journals Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe

2013 ◽  
Vol 82 (2) ◽  
pp. 216-229 ◽  
Author(s):  
Shiva Bhowmik ◽  
David H. Jones ◽  
Hsien‐Po Chiu ◽  
In‐Hee Park ◽  
Hsiu‐Ju Chiu ◽  
...  
Keyword(s):  
Bile Acid ◽  
Functional Characterization ◽  
Acid Synthesis ◽  
Bile Acid Synthesis ◽  
Human Gut ◽  
Secondary Bile Acid ◽  
Gut Microbe

scholarly journals Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens

2013 ◽  
Vol 54 (9) ◽  
pp. 2437-2449 ◽  
Author(s):  
Jason M. Ridlon ◽  
Shigeo Ikegawa ◽  
João M. P. Alves ◽  
Biao Zhou ◽  
Akiko Kobayashi ◽  
...  
Keyword(s):  
High Potential ◽  
Human Gut ◽  
Gut Microbe
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