The Microbiome’s Function in Disorders of the Urinary Bladder

The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods.

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Urinary Microbiome: Yin and Yang of the Urinary Tract

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.617002 ◽

2021 ◽

Vol 11 ◽

Author(s):

Virginia Perez-Carrasco ◽

Ana Soriano-Lerma ◽

Miguel Soriano ◽

José Gutiérrez-Fernández ◽

Jose A. Garcia-Salcedo

Keyword(s):

Urinary Tract ◽

Treatment Strategies ◽

Opportunistic Pathogens ◽

Current State ◽

Urinary Microbiome ◽

Yin And Yang ◽

Health And Disease ◽

Tract Infections ◽

Generation Sequencing

The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.

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Next-generation sequencing-based molecular characterization of primary urinary bladder adenocarcinoma

Modern Pathology ◽

10.1038/modpathol.2017.33 ◽

2017 ◽

Vol 30 (8) ◽

pp. 1133-1143 ◽

Cited By ~ 18

Author(s):

Somak Roy ◽

Dinesh Pradhan ◽

Wayne L Ernst ◽

Stephanie Mercurio ◽

Yana Najjar ◽

...

Keyword(s):

Next Generation Sequencing ◽

Urinary Bladder ◽

Molecular Characterization ◽

Next Generation ◽

Bladder Adenocarcinoma ◽

Generation Sequencing

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Rhizosphere Microbial Community Dynamics in Glyphosate-Treated Susceptible and Resistant Biotypes of Giant Ragweed (Ambrosia trifida)

Weed Science ◽

10.1614/ws-d-13-00164.1 ◽

2014 ◽

Vol 62 (2) ◽

pp. 370-381 ◽

Cited By ~ 8

Author(s):

Jessica R. Schafer ◽

Steven G. Hallett ◽

William G. Johnson

Keyword(s):

Microbial Community ◽

Next Generation Sequencing ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Microbial Interactions ◽

Field Soil ◽

Next Generation ◽

Giant Ragweed ◽

Generation Sequencing ◽

Rhizosphere Microbial Community

In a previous study, glyphosate-susceptible and -resistant giant ragweed biotypes grown in sterile field soil survived a higher rate of glyphosate than those grown in unsterile field soil, and the roots of the susceptible biotype were colonized by a larger number of soil microorganisms than those of the resistant biotype when treated with 1.6 kg ae ha−1glyphosate. Thus, we concluded that soil-borne microbes play a role in glyphosate activity and now hypothesize that the ability of the resistant biotype to tolerate glyphosate may involve microbial interactions in the rhizosphere. The objective of this study was to evaluate differences in the rhizosphere microbial communities of glyphosate-susceptible and -resistant giant ragweed biotypes 3 d after a glyphosate treatment. Giant ragweed biotypes were grown in the greenhouse in unsterile field soil and glyphosate was applied at either 0 or 1.6 kg ha−1. Rhizosphere soil was sampled 3 d after the glyphosate treatment, and DNA was extracted, purified, and sequenced with the use of Illumina Genome Analyzer next-generation sequencing. The taxonomic distribution of the microbial community, diversity, genera abundance, and community structure within the rhizosphere of the two giant ragweed biotypes in response to a glyphosate application was evaluated by metagenomics analysis. Bacteria comprised approximately 96% of the total microbial community in both biotypes, and differences in the distribution of some microbes at the phyla level were observed. Select soil-borne plant pathogens (VerticilliumandXanthomonas) and plant-growth–promoting rhizobacteria (Burkholderia) present in the rhizosphere were influenced by either biotype or glyphosate application. We did not, however, observe large differences in the diversity or structure of soil microbial communities among our treatments. The results of this study indicate that challenging giant ragweed biotypes with glyphosate causes perturbations in rhizosphere microbial communities and that the perturbations differ between the susceptible and resistant biotypes. However, biological relevance of the rhizosphere microbial community data that we obtained by next-generation sequencing remains unclear.

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Next-generation Sequencing Generated Discrepancy in Abundance Characterization of Complex Microbial Community Compositions： an Error of Bioinformatics Pipeline

Proceedings of 2017 the 7th International Workshop on Computer Science and Engineering ◽

10.18178/wcse.2017.06.238 ◽

2017 ◽

Keyword(s):

Microbial Community ◽

Next Generation Sequencing ◽

Next Generation ◽

Bioinformatics Pipeline ◽

Complex Microbial Community ◽

Generation Sequencing

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Characterization of The Microbiome That Colonizes The Digestive Tract of Calves From 0 To 42 Days of Age, Raised In The Mexican Tropics.

10.21203/rs.3.rs-741679/v1 ◽

2021 ◽

Author(s):

Carolina Robles Rodríguez ◽

María Laura González Dávalos ◽

Armando Shimada ◽

Carla Daniela Robles Espinoza ◽

Maria Ofelia Mora

Keyword(s):

Next Generation Sequencing ◽

Gastrointestinal Tract ◽

Microbial Communities ◽

Digestive System ◽

Diversity Analysis ◽

Alpha And Beta Diversity ◽

Sequencing Platforms ◽

Generation Sequencing ◽

Mexican Tropics

Abstract In the first few weeks of a calf's life, the early colonization of microbes throughout the gastrointestinal tract (GIT) is critical in its digestive system and immunity development. Analyses of data generated from next-generation sequencing platforms have revolutionized the understanding of host-associated microbial communities; these analyses can be done through a variety of bioinformatics pipelines. This study aimed to describe the diversity and evolution of gastrointestinal tract microbial communities in the first days of life of calves; for which we used the USEARCH and KRAKEN2 algorithms, in terms of alpha and beta diversity analysis in the rumen and jejunum contents of calves from 0, 7, 28, 42 days-born in the Mexican Tropic and its changes. The two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. The present study revealed the changes occurring in the rumen and jejunum ecosystem in the first week of life, reflected by a decline in the phylum Proteobacteria and an increase in phylum Bacteroidetes in rumen and Firmicutes in the jejunum. We observed an increase in the similarity in the phylum taxa with age, suggesting a homogeneous and specific mature community, compared with the primary community.

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