International consensus statement on microbiome testing in clinical practice.

There is growing interest in the potential exploitation of the gut microbiome as a diagnostic tool in medicine, but evidence supporting its clinical usefulness is scarce. An increasing number of commercial providers offer direct-to-consumer microbiome diagnostic tests without any consensus on their regulation or any proven value in clinical practice, which could result in considerable waste of individual and health-care resources and potential drawbacks in the clinical management of patients. We convened an international multidisciplinary expert panel to standardise best practices of microbiome testing for clinical implementation, including recommendations on general principles and minimum requirements for their provision, indications, pre-testing protocols, method of analyses, reporting of results, and potential clinical value.

Healthy and Unhealthy Aging and the Human Microbiome.

An altered gut microbiome is a feature of many multifactorial diseases, and microbiome effects on host metabolism, immune function, and possibly neurological function are implicated. Increased biological age is accompanied by a change in the gut microbiome. However, age-related health loss does not occur uniformly across all subjects but rather depends on differential loss of gut commensals and gain of pathobionts.

Yeast -glucan supplementation lowers insulin resistance without altering microbiota composition compared with placebo in subjects with type II diabetes: a phase I exploratory study.

The increased global prevalence of type II diabetes mellitus (T2DM) is associated with consumption of low fibre 'Western diets'. Characteristic metabolic parameters of these individuals include insulin resistance, high fasting and postprandial glucose, as well as low-grade systemic inflammation. Gut microbiota composition is altered significantly in these cohorts suggesting a causative link between diet, microbiota and disease.

Genome sequence of the New Zealand raw milk isolate and candidate probiotic strain FNZ339.

The complete genome sequence of the candidate probiotic strain FNZ339 was determined using a hybrid genome assembly comprising data from Illumina and Oxford Nanopore Technologies sequencing platforms. The genome assembly comprised 2,673,297 bp, including the complete circular chromosome and four circular plasmids.

Genome sequence of the New Zealand cheese isolate and candidate probiotic strain FNZ042.

The complete genome sequence of the candidate probiotic strain FNZ042 was determined using a hybrid genome assembly comprising data from Illumina and PacBio sequencing platforms. The genome assembly comprised 3,265,637 bp, including the complete circular chromosome and three circular plasmids.

Cross-Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment.

Irritable bowel syndrome (IBS) is a prevalent disorder of gut-brain interaction without a reliable cure. Evidence suggests that an alteration of the gut microbiome may contribute to IBS pathogenesis, motivating the development of microbiome-targeted therapies to alleviate IBS symptoms. However, IBS-specific microbiome signatures are variable across cohorts.

Disease-associated microbiome signature species in the gut.

There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (sometimes called ) associates with risk for many noncommunicable diseases. However, the dynamics of disease-linked bacteria in the gut and other body sites remain unclear. If microbiome alterations prove causative in particular diseases, therapeutic intervention may be possible.

Ageing, microbes and health.

The human gut microbiome is a modifier of the risk for many non-communicable diseases throughout the lifespan. In ageing, the effect of the microbiome appears to be more pronounced because of the lower physiological reserve. Microbial metabolites and other bioactive products act upon some of the key physiological processes involved in the Hallmarks of Ageing.

Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables.

Unlabelled: Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations ( = 241).

Microbe Profile: The .

The bacterial family (the lactobacilli) occupy a unique role in microbiology due to their beneficial role in both human cultural history and biology, from the food preservation of hunter gatherers-turned-farmers, through the prevention of scurvy in seafarers exploring new worlds, and the health-promoting properties of species that colonize the human body as well as animals that are important for agriculture and pollination. The almost bewildering phenotypic and genomic complexity of the former genus was recently reconciled with molecular taxonomy and phylogeny to establish robust genera comprising the , whose main features are summarized in this Microbe Profile.

Comparative diet-gut microbiome analysis in Crohn's disease and Hidradenitis suppurativa.

Introduction: The chronic inflammatory skin disease Hidradenitis suppurativa (HS) is strongly associated with Crohn's Disease (CD). HS and CD share clinical similarities and similar inflammatory pathways are upregulated in both conditions. Increased prevalence of inflammatory disease in industrialised nations has been linked to the Western diet.

Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model.

Human aging is characterized by gut microbiome alteration and differential loss of gut commensal species associated with the onset of frailty. The administration of cultured commensal strains to replenish lost taxa could potentially promote healthy aging. To investigate the interaction of whole microbiomes and administered strains, we transplanted gut microbiota from a frail or healthy elderly subject into germ-free mice.

gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Isolated from the Human Gut and Proposal of the Novel Family fam. nov.

The methanogenic strain Mx-05 was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order . It shares 86.

Associations between host microbiome and inflammation suggest role for host microbiome in driving COVID-19 disease severity.

Systemic inflammation and innate immune activation are associated with COVID-19 disease severity. Knowledge gaps remain in the relationships between microbiome, inflammation and COVID-19 disease severity. To better characterise these associations, we performed 16SrDNA analysis of stool samples in COVID-19 subjects to explore diversity and taxanomic composition.

Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways.

A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow's milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species or the sub-species subsp, subsp or subsp in each kefir.

Robust cross-cohort gut microbiome associations with COVID-19 severity.

Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences.

'Good, honest food': older adults' and healthcare professionals' perspectives of dietary influences and food preferences in older age in Ireland.

Background: This study aimed to explore older adults' and healthcare professionals' (HCPs) perceptions of dietary influences and food preferences in older age.

Methods: The research design was phenomenological qualitative description. Semistructured one-to-one interviews and focus groups were held separately with community-dwelling older adults and HCPs involved in care of the older person in Ireland.

Toward an improved definition of a healthy microbiome for healthy aging.

The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance.

Human microbiome variance is underestimated.

Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living in socioeconomically developed countries.

Older adults and healthcare professionals have limited awareness of the link between the Mediterranean diet and the gut microbiome for healthy aging.

Objectives: Strategies to improve the gut microbiome through consuming an improved diet, including adopting the Mediterranean Diet (MD), may promote healthy aging. We explored older adults' and healthcare professionals' (HCPs) perspectives of the MD, gut health, and microbiome for their role in healthy aging.

Design: Phenomenological qualitative.