scholarly journals Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement

2021 ◽  
Vol 9 (5) ◽  
pp. 892
Author(s):  
Stina Hedžet ◽  
Maja Rupnik ◽  
Tomaž Accetto
Keyword(s):  
Gut Microbiota ◽  
Outer Membrane Proteins ◽  
Human Microbiome ◽  
Human Gut ◽  
Amino Acid Similarity ◽  
Gene Encoding ◽  
Sequence Variations ◽  
Bacterial Groups ◽  
Putative Phage ◽  
Host Genes

Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.

scholarly journals Lytic Bacteroides uniformis bacteriophages exhibiting host tropism congruent with diversity generating retroelement

2020 ◽  
Author(s):  
Stina Hedzet ◽  
Tomaž Accetto ◽  
Maja Rupnik
Keyword(s):  
Gut Microbiota ◽  
Outer Membrane Proteins ◽  
Marker Gene ◽  
Human Microbiome ◽  
Host Tropism ◽  
Sequence Variations ◽  
Common Marker ◽  
Evolutionary Advantage ◽  
Bacterial Groups

AbstractIntestinal phages are abundant and important component of gut microbiota, but our knowledge remains limited to only a few isolated and characterized representatives targeting numerically dominant gut bacteria. Here we describe isolation of human intestinal phages infecting Bacteroides uniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota, however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within Siphoviridae family and represent the first lytic phages, genomes of which encode diversity generating retroelements (DGR). This region is assumed to promote phage adaptation to the rapidly changing environmental conditions and to broaden its host range. Three isolated phages showed 99,83% genome identity but infected distinct B. uniformis strains. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% aa similarity to Bacuni phages in the genomes of B. acidifaciens and Prevotella sp.. Despite the abundance of Bacteroides within human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.ImportanceThe lack of common marker gene in viruses require a precise characterization of diverse isolated phages to enhance metagenomic analyses and to understand their role in gut microbiota. Here we report the isolation of phages representing a new genus with characteristics so far not known or rarely described in intestinal phages. They are the first lytic phages specific for Bacteroides uniformis, a bacterial representative of the prevalent genus in the gut of humans and animals. Additionally, they are the first lytic phages containing specific regions (diversity generating retroelement) that putatively influence host tropism. The ability to switch constantly the targeted populations of the host species could provide an evolutionary advantage to these bacteriophages and may affect intra species diversity.

scholarly journals Gut SymbiontBacteroides fragilisSecretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Maria Chatzidaki-Livanis ◽  
Michael J. Coyne ◽  
Kevin G. Roelofs ◽  
Rahul R. Gentyala ◽  
Jarreth M. Caldwell ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacteroides Fragilis ◽  
Signal Peptidase ◽  
Metagenomic Data ◽  
Antimicrobial Protein ◽  
Secretion Systems ◽  
Human Gut ◽  
Gene Encoding ◽  
Toxic Activity ◽  
Signal Peptidase I

ABSTRACTHuman gutBacteroidesspecies produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains ofBacteroides fragilissecrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidalessecreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced byB. fragilisstrain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset ofB. fragilisstrains. The addition ofubbinto a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in theB. fragilisgenome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed thatubbis present in 12% of the metagenomes that have evidence ofB. fragilis. As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40B. fragilisstrains, revealing that 75% ofB. fragilisstrains are targeted by one or the other of these two secreted proteins of strain 638R.IMPORTANCEWe are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundantBacteroidesspecies. Here, we show that some strains ofBacteroides fragilishave acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against otherB. fragilisstains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.

Complementary Functional Strategy for Modulation of Human Gut Microbiota

2019 ◽  
Vol 24 (35) ◽  
pp. 4144-4149 ◽  
Author(s):  
Emanuel Vamanu
Keyword(s):  
Gut Microbiota ◽  
Human Microbiome ◽  
Edible Mushrooms ◽  
Alternative Methods ◽  
Wild Edible Mushrooms ◽  
Human Gut ◽  
Mushroom Species ◽  
Innovative Strategies ◽  
Functional Strategy ◽  
Complementary Strategy

Two pathologies commonly associated with gut microbiota dysbiosis are type 2 diabetes and cardiovascular diseases. Since diet and medication are two important causes of microbiome fingerprint modifications, new complementary and alternative methods can include wild edible mushrooms, which serve as functional products, given their properties in modulating the microbial pattern at the colon level. A disturbance in microbial balance translates into the occurrence of degenerative dysfunctions that are also associated with other pathologies, such as obesity, colon cancer. The metagenomic study has enabled the identification of some competitive microbiological and biochemical biomarkers which allow the development of innovative strategies in controling microbial disbalance from human gut. Thus, the aim of this review was to present the significant findings related to human microbiome modulation via the prebiotic effects of wild edible mushrooms as a complementary strategy to modern treatment. Certain mushroom species have been approached and their effects on the microbiota fingerprint of two major target groups are highlighted.

GUT Microbiome-GUT Dysbiosis-Arterial Hypertension: New Horizons

2019 ◽  
Vol 15 (1) ◽  
pp. 40-46 ◽  
Author(s):  
Vasiliki Katsi ◽  
Matthaios Didagelos ◽  
Stamatios Skevofilax ◽  
Iakovos Armenis ◽  
Athanasios Kartalis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Arterial Hypertension ◽  
Animal Studies ◽  
Human Microbiome ◽  
Bioactive Metabolites ◽  
Human Gut ◽  
Fecal Microbiome ◽  
New Horizons ◽  
Blood Pressure Homeostasis ◽  
Treatment Responsiveness

Arterial hypertension is a progressive cardiovascular syndrome arising from complex and interrelated etiologies. The human microbiome refers to the community of microorganisms that live in or on the human body. They influence human physiology by interfering in several processes such as providing nutrients and vitamins in Phase I and Phase II drug metabolism. The human gut microbiota is represented mainly by Firmicutes and Bacteroidetes and to a lesser degree by Actinobacteria and Proteobacteria, with each individual harbouring at least 160 such species. Gut microbiota contributes to blood pressure homeostasis and the pathogenesis of arterial hypertension through production, modification, and degradation of a variety of microbial-derived bioactive metabolites. Animal studies and to a lesser degree human research has unmasked relative mechanisms, mainly through the effect of certain microbiome metabolites and their receptors, outlining this relationship. Interventions to utilize these pathways, with probiotics, prebiotics, antibiotics and fecal microbiome transplantation have shown promising results. Personalized microbiome-based disease prediction and treatment responsiveness seem futuristic. Undoubtedly, a long way of experimental and clinical research should be pursued to elucidate this novel, intriguing and very promising horizon.

In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
C Moissl-Eichinger ◽  
R Bauer
Keyword(s):  
Gut Microbiota ◽  
In Vitro Study ◽  
Vitro Study ◽  
Bark Extract ◽  
Herbal Extracts ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Willow Bark

Metabolization of the herbal combination STW-5 by human gut microbiota in vitro

2017 ◽  
Author(s):  
EM Pferschy-Wenzig ◽  
A Roßmann ◽  
K Koskinen ◽  
H Abdel-Aziz ◽  
C Moissl-Eichinger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota

Substrate use prioritization by a coculture of five species of gut bacteria fed mixtures of arabinoxylan, xyloglucan, β-glucan, and pectin

2020 ◽  
Author(s):  
Y Liu ◽  
AL Heath ◽  
B Galland ◽  
N Rehrer ◽  
L Drummond ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Plant Cell Wall ◽  
Bacterial Species ◽  
Short Chain ◽  
Emergent Properties ◽  
Human Gut ◽  
Fermentation Products ◽  
Plant Polysaccharides ◽  
Human Gut Microbiota

© 2020 American Society for Microbiology. Dietary fiber provides growth substrates for bacterial species that belong to the colonic microbiota of humans. The microbiota degrades and ferments substrates, producing characteristic short-chain fatty acid profiles. Dietary fiber contains plant cell wall-associated polysaccharides (hemicelluloses and pectins) that are chemically diverse in composition and structure. Thus, depending on plant sources, dietary fiber daily presents the microbiota with mixtures of plant polysaccharides of various types and complexity. We studied the extent and preferential order in which mixtures of plant polysaccharides (arabinoxylan, xyloglucan, β-glucan, and pectin) were utilized by a coculture of five bacterial species (Bacteroides ovatus, Bifidobacterium longum subspecies longum, Megasphaera elsdenii, Ruminococcus gnavus, and Veillonella parvula). These species are members of the human gut microbiota and have the biochemical capacity, collectively, to degrade and ferment the polysaccharides and produce short-chain fatty acids (SCFAs). B. ovatus utilized glycans in the order β-glucan, pectin, xyloglucan, and arabinoxylan, whereas B. longum subsp. longum utilization was in the order arabinoxylan, arabinan, pectin, and β-glucan. Propionate, as a proportion of total SCFAs, was augmented when polysaccharide mixtures contained galactan, resulting in greater succinate production by B. ovatus and conversion of succinate to propionate by V. parvula. Overall, we derived a synthetic ecological community that carries out SCFA production by the common pathways used by bacterial species for this purpose. Systems like this might be used to predict changes to the emergent properties of the gut ecosystem when diet is altered, with the aim of beneficially affecting human physiology. This study addresses the question as to how bacterial species, characteristic of the human gut microbiota, collectively utilize mixtures of plant polysaccharides such as are found in dietary fiber. Five bacterial species with the capacity to degrade polymers and/or produce acidic fermentation products detectable in human feces were used in the experiments. The bacteria showed preferential use of certain polysaccharides over others for growth, and this influenced their fermentation output qualitatively. These kinds of studies are essential in developing concepts of how the gut microbial community shares habitat resources, directly and indirectly, when presented with mixtures of polysaccharides that are found in human diets. The concepts are required in planning dietary interventions that might correct imbalances in the functioning of the human microbiota so as to support measures to reduce metabolic conditions such as obesity.

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