Metabolic and enzymatic elucidation of cooperative degradation of red seaweed agarose by two human gut bacteria

AbstractVarious health beneficial outcomes associated with red seaweeds, especially their polysaccharides, have been claimed, but the molecular pathway of how red seaweed polysaccharides are degraded and utilized by cooperative actions of human gut bacteria has not been elucidated. Here, we investigated the enzymatic and metabolic cooperation between two human gut symbionts, Bacteroides plebeius and Bifidobacterium longum ssp. infantis, with regard to the degradation of agarose, the main carbohydrate of red seaweed. More specifically, B. plebeius initially decomposed agarose into agarotriose by the actions of the enzymes belonging to glycoside hydrolase (GH) families 16 and 117 (i.e., BpGH16A and BpGH117) located in the polysaccharide utilization locus, a specific gene cluster for red seaweed carbohydrates. Then, B. infantis extracted energy from agarotriose by the actions of two agarolytic β-galactosidases (i.e., Bga42A and Bga2A) and produced neoagarobiose. B. plebeius ultimately acted on neoagarobiose by BpGH117, resulting in the production of 3,6-anhydro-l-galactose, a monomeric sugar possessing anti-inflammatory activity. Our discovery of the cooperative actions of the two human gut symbionts on agarose degradation and the identification of the related enzyme genes and metabolic intermediates generated during the metabolic processes provide a molecular basis for agarose degradation by gut bacteria.

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If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria

Journal of Bacteriology ◽

10.1128/jb.00481-20 ◽

2020 ◽

Author(s):

Robert W.P. Glowacki ◽

Eric C. Martens

Keyword(s):

Synthetic Biology ◽

Nutrient Utilization ◽

Gut Bacteria ◽

Maillard Reaction Products ◽

Reaction Products ◽

Human Gut ◽

Host Diet ◽

Health And Disease ◽

Gut Symbionts ◽

Polysaccharide Utilization Loci

In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria. Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.

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Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria

10.1101/2020.06.09.142968 ◽

2020 ◽

Author(s):

Nicholas A. Pudlo ◽

Gabriel Vasconcelos Pereira ◽

Jaagni Parnami ◽

Melissa Cid ◽

Stephanie Markert ◽

...

Keyword(s):

Future Generation ◽

Gut Bacteria ◽

Mobile Dna ◽

Terrestrial Plants ◽

Human Gut ◽

Edible Seaweed ◽

Edible Macroalgae ◽

Dna Elements ◽

Gut Symbionts ◽

Global Exchange

SummaryHumans harbor numerous species of colonic bacteria that digest the fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients and use these abilities to colonize microbiomes around the world, especially outside Asia. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Using culture-based approaches, we show that known Bacteroides genes involved in seaweed degradation have mobilized into many members of this genus. We also identify several previously unknown examples of marine bacteria-derived genes, and their corresponding mobile DNA elements, that are involved in degrading seaweed polysaccharides. Some of these genes reside in gut-resident, Gram-positive Firmicutes, for which phylogenetic analysis suggests an origin in the Epulopiscium gut symbionts of marine fishes. Our results are important for understanding the metabolic plasticity of the human gut microbiome, the global exchange of genes in the context of dietary selective pressures and identifying new functions that can be introduced or engineered to design and fill orthogonal niches for a future generation of engineered probiotics.

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Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts

10.1101/2020.05.22.111492 ◽

2020 ◽

Author(s):

Leonor García-Bayona ◽

Michael J. Coyne ◽

Noam Hantman ◽

Paula Montero-Llopis ◽

Salena Von ◽

...

Keyword(s):

Gut Microbiota ◽

Stress Responses ◽

Fluorescent Proteins ◽

Gut Bacteria ◽

Mucus Layer ◽

Human Gut ◽

Terminal Electron Acceptor ◽

Cellular Processes ◽

Dynamic Type ◽

Gut Symbionts

AbstractMechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular processes in actively growing bacteria. Although underappreciated, many gut “anaerobes” are able to respire using oxygen as the terminal electron acceptor. The oxygen continually released from gut epithelial cells creates an oxygen gradient from the mucus layer to the anaerobic lumen (1), with oxygen available to bacteria growing at the mucus layer. Using a combination of analyses, we show that Bacteroides species are metabolically and energetically robust and do not mount stress responses in the presence of 0.10 - 0.14% oxygen, defined as nanaerobic conditions (2). Taking advantage of this metabolic capability, we show that nanaerobic growth provides sufficient oxygen for the maturation of oxygen-requiring fluorescent proteins in Bacteroides species. Type strains of four different Bacteroides species show bright GFP fluorescence when grown nanaerobically versus anaerobically. We compared four different red fluorescent proteins and found that mKate2 yields high fluorescence intensity in our assay. We show that GFP-tagged proteins can be localized in nanaerobically growing bacteria. In addition, we used time-lapse fluorescence microscopy to image dynamic Type VI secretion system processes in metabolically active B. fragilis. The ability to visualize fluorescently-labeled Bacteroides and fluorescently-linked proteins in actively growing nanaerobic gut symbionts ushers in a new age of imaging analyses in these bacteria.SignificanceDespite many recent technological advances to study the human gut microbiota, we still lack a facile system to image dynamic cellular processes in most abundant gut species due to the requirement of oxygen for chromophore maturation of commonly used fluorescent proteins. Here, we took advantage of the ability of anaerobes of the gut microbiota to respire aerobically and grow robustly at 0.10– 0.14% oxygen. This physiologic concentration of oxygen is sufficient for fluorescent proteins to mature, allowing for visualization of biological processes never before imaged in these bacteria. This advance will allow for numerous types of analyses in actively-growing “nanaerobic” gut bacteria including subcellular protein localizations, single-cell analyses, biofilm imaging, and protein interactions with other microbes and the host.

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Combining LC-MS metabolomics and next generation sequencing to study the interactions between herbal medicines and human gut bacteria in-vitro

10.1055/s-0037-1608574 ◽

2017 ◽

Author(s):

EM Pferschy-Wenzig ◽

K Koskinen ◽

A Roßmann ◽

K Ardjomand-Woelkart ◽

C Moissl-Eichinger ◽

...

Keyword(s):

Next Generation Sequencing ◽

Herbal Medicines ◽

Gut Bacteria ◽

Next Generation ◽

Human Gut ◽

Generation Sequencing

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Faculty Opinions recommendation of Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718118305.793485814 ◽

2013 ◽

Author(s):

Jo Handelsman ◽

Heather Allen

Keyword(s):

Gut Bacteria ◽

Functional Metagenomics ◽

Human Gut

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Faculty Opinions recommendation of Human gut bacteria contain acquired interbacterial defence systems.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736828921.793567257 ◽

2019 ◽

Author(s):

Michael Kurilla

Keyword(s):

Gut Bacteria ◽

Human Gut

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Design, Synthesis and Bioactivity of Core 1 O-glycan and its Derivative on Human Gut Microbiota

Letters in Drug Design & Discovery ◽

10.2174/1570180816666181218143207 ◽

2019 ◽

Vol 16 (12) ◽

pp. 1348-1353

Author(s):

Huanhuan Qu ◽

Baixue Li ◽

Jingyi Yang ◽

Huaiwen Liang ◽

Meixia Li ◽

...

Keyword(s):

Gut Microbiota ◽

Initial Step ◽

Building Blocks ◽

Glycan Structure ◽

Human Gut ◽

Design Synthesis ◽

The Core ◽

Human Gut Microbiota ◽

Biochemical Studies ◽

Gut Symbionts

Background: Disaccharide core 1 (Galβ1-3GalNAc) is a common O-glycan structure in nature. Biochemical studies have confirmed that the formation of the core 1 structure is an important initial step in O-glycan biosynthesis and it is of great importance for human body. Objective: Our study will provide meaningful and useful sights for O-glycan synthesis and their bioassay. And all the synthetic glycosides would be used as intermediate building blocks in the scheme developed for oligosaccharide construction. Methods: In this article, we firstly used chemical procedures to prepare core 1 and its derivative, and a novel disaccharide was efficiently synthesized. The structures of the synthesized compounds were elucidated and confirmed by 1H NMR, 13C NMR and MS. Then we employed three human gut symbionts belonging to Bacteroidetes, a predominantphyla in the distal gut, as models to study the bioactivity of core 1 and its derivative on human gut microbiota. Results: According to our results, both core 1 and derivative could support the growth of B. fragilis, especially the core 1 derivative, while failed to support the growth of B. thetaiotaomicron and B. ovatus. Conclusion: This suggested that the B. fragilis might have the specificity glycohydrolase to cut the glycosidic bond for acquiring monosaccharide.

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Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽

10.3390/nu13082688 ◽

2021 ◽

Vol 13 (8) ◽

pp. 2688

Author(s):

Tobias Goris ◽

Rafael R. C. Cuadrat ◽

Annett Braune

Keyword(s):

Gut Microbiome ◽

Large Scale ◽

Health Impact ◽

Gut Bacteria ◽

Human Gut ◽

Positive Health ◽

Human Gut Microbiome ◽

Nutritional Recommendations ◽

Genes Encoding ◽

A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

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