Microbiota and kidney disease: the road ahead.

More than 850 million individuals worldwide, accounting for 10-15% of the adult population, are estimated to have chronic kidney disease. Each of these individuals is host to tens of trillions of microorganisms that are collectively referred to as microbiota - a dynamic ecosystem that both influences host health and is itself influenced by changes in the host. Available evidence supports the existence of functional connections between resident microorganisms and kidney health that are altered in the context of specific kidney diseases, including acute kidney injury, chronic kidney disease and renal stone disease.

Inducing Colonization Reduces Urinary Oxalate in Healthy Adults.

Introduction: Oxalate-degrading intestinal bacteria, including the oxalate-degrading specialist, have the potential to reduce urinary oxalate excretion in humans, and thus limit the risk of calcium oxalate kidney stone formation. The aim of this proof-of-concept study, which was performed in healthy adults, was to demonstrate that ingestion of live is safe, can establish sustainable gut colonization, and reduce urinary oxalate excretion.

Methods: Twenty-two healthy adults without a history of kidney stones and not colonized with ingested diets controlled in oxalate and calcium.

Urine microbiome profiles in patients with different types of kidney stones.

Kidney stone disease (KSD) is a multifactorial condition influenced by systemic and extrinsic factors, including diet, genetics, metabolic disorders, and microbial and environmental factors. Although preliminary evidence links the urinary microbiome (UMB) to stone formation, its role in different stone types remains unclear. We analysed UMB in patients with four distinct types of kidney stones (calcium oxalate, struvite, uric acid, and mixed composition).

Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.

The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases.

Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria.

Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate.

Antimicrobial resistance and biofilm formation of penile prosthesis isolates: insights from in-vitro analysis.

Background: Inflatable penile prostheses (IPPs) have been shown to harbor biofilms in the presence and absence of infection despite exposure to various antimicrobials. Microbes persisting on IPPs following antibiotic exposure have not been adequately studied to assess biofilm formation capacity and antibiotic resistance.

Aim: In this study, we aimed to assess these properties of microbes obtained from explanted infected and non-infected IPPS using an in vitro model.

Deciphering Sperm-Carried IGF2 Transcript Variants: Cloning, qPCR Detection, and Variant Analysis.

Context: The insulin-like growth factor 2 (IGF2) gene, a paternally imprinted gene inactive in oocytes, plays a vital role in early embryo development. While 5 IGF2 variants have been described, the specific variants expressed in human spermatozoa compared to granulosa cells (GCs) remain unclear.

Objective: To characterize the quantity and variants of IGF2 transcripts expressed in human spermatozoa.

Mechanism of Nephrolithiasis: Does the Microbiome Play a Role?

Nephrolithiasis imposes a significant health care burden around the world. In the past decade, there has been considerable interest in the human microbiota in relation to the onset of nephrolithiasis. Most of the research has focused on degradation of oxalate, a known causative factor for nephrolithiasis, by bacteria in the gut.

Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria.

Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate.

An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.

Purpose: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response.

Dysbiosis of the oral microbiota composition is associated with oral squamous cell carcinoma and the impact of radiotherapy: a pilot study.

Radiotherapy can potentially influence the diversity and composition of the oral microbiome. We performed a study comparing the composition of oral microbiota in patients with oral squamous cell carcinoma (OSCC) before radiotherapy (n = 6), at three months (n = 6), and six months (n = 6) post-radiotherapy, and controls (n = 6). We profiled the oral microbiome by 16S rRNA gene sequencing using Illumina MiSeq.

Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease.

In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear.

Whole genome sequence analysis and in-vitro probiotic characterization of Bacillus velezensis FCW2 MCC4686 from spontaneously fermented coconut water.

In this study, the probiotic potential of B. velezensis FCW2, isolated from naturally fermented coconut water, was investigated by in vitro and genomic characterization. Our findings highlight key features of the bacterium which includes, antibacterial activity, high adhesive potential, aggregation capacity, production of nutrient secondary metabolites.

Genomic and metabolic properties of Staphylococcus gallinarum FCW1 MCC4687 isolated from naturally fermented coconut water towards GRAS assessment.

Staphylococcus gallinarum FCW1 was isolated from naturally fermented coconut-water and identified by biochemical and molecular methods. Probiotic characterization and safety assessment were conducted through a series of in vitro tests. A high survival rate was observed when the strain was tested for resistance to bile, lysozyme, simulated gastric and intestinal fluid, phenol, and different temperature and salt concentrations.

Bacterial diversity of traditional fermented food, by high thorough-put sequencing.

Unlabelled: The bacterial composition of naturally fermented Indian food, was studied by high-throughput Illumina amplicon sequencing at different taxonomic levels. Metagenomic investigation revealed fold change with respect to some of the phylotypes in 06 to 12 h of fermentation, suggesting the synergistic mode of nutrition. After 12 h fermentation, bacterial populations were stabilized towards 15 h fermentation.

Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition.

To determine whether functionally relevant questions associated with the urinary or gut microbiome and urinary stone disease (USD) can be answered from metagenome-wide association studies (MWAS), we performed the most comprehensive meta-analysis of published clinical MWAS in USD to date, using publicly available data published prior to April 2021. Six relevant studies met inclusion criteria. For alpha-diversity, significant differences were noted between USD status, stone composition, sample type, study location, age, diet, and sex.

Standardization of microbiome studies for urolithiasis: an international consensus agreement.

Numerous metagenome-wide association studies (MWAS) for urolithiasis have been published, leading to the discovery of potential interactions between the microbiome and urolithiasis. However, questions remain about the reproducibility, applicability and physiological relevance of these data owing to discrepancies in experimental technique and a lack of standardization in the field. One barrier to interpreting MWAS is that experimental biases can be introduced at every step of the experimental pipeline, including sample collection, preservation, storage, processing, sequencing, data analysis and validation.

Species - An Imminent Resource to Explore Biosurfactant and Bioactive Metabolites for Industrial Applications.

The marine environment represents a well-off and diverse group of microbes, which offers an enormous natural bioactive compounds of commercial importance. These natural products have expanded rigorous awareness due to their widespread stability and functionality under harsh environmental conditions. The genus is a halophilic bacterium known for the production of diverse secondary metabolites such as 2-acetamido-2-deoxy-α-d-glucopyranosyl-(1, 2)-β-d-fructofuranose exhibiting stabilizing effect and methyl glucosyl-3,4-dehydro-apo-8-lycopenoate displaying antioxidant activity.

Human microbiome: an academic update on human body site specific surveillance and its possible role.

Human body is inhabited by vast number of microorganisms which form a complex ecological community and influence the human physiology, in the aspect of both health and diseases. These microbes show a relationship with the human immune system based on coevolution and, therefore, have a tremendous potential to contribute to the metabolic function, protection against the pathogen and in providing nutrients and energy. However, of these microbes, many carry out some functions that play a crucial role in the host physiology and may even cause diseases.

Data on genome sequencing, assembly, annotation and genomic analysis of strain SPC17 isolated from Lonar Lake.

The bacterial isolates of genus are best known for their significant biodegradation abilities. Here, we report the data related to draft genome sequencing of strain SPC17 isolated from sediments of Lonar Lake. The assembly of 1598096 Illumina's paired-end sequencing reads resulted in 51 contigs for an overall genome assembly size of 4.

Exploring the Pharmacological Potentials of Biosurfactant Derived from Planococcus maritimus SAMP MCC 3013.

Therapeutic potential of biosurfactant (BS) has been improved in recent years. Our present study deals with production of BS from Planococcus maritimus SAMP MCC 3013 in a mineral salt medium (MSM) supplemented with glucose (1.5% w/v).

Author Correction: Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Diversity and Succession of Microbiota during Fermentation of the Traditional Indian Food Idli.

Idli, a naturally fermented Indian food, is prepared from a mixture of rice and black gram (lentil). To understand its microbial community during fermentation, detailed analysis of the structural and functional dynamics of the idli microbiome was performed by culture-dependent and -independent approaches. The bacterial diversity and microbial succession were assessed at different times of fermentation by 16S rRNA amplicon sequencing.

Microcosm study of atrazine bioremediation by indigenous microorganisms and cytotoxicity of biodegraded metabolites.

Intensive use of atrazine in agriculture to increase crop productivity has resulted in pollution and consequently deteriorated the environment. Three isolated bacteria, Rhodococcus sp. BCH2 (RB), Bacillus sp.