Fecal microbiota composition and frailty

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic

Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species. In this study, we described a protocol to isolate novel F. prausnitzii strains from feces of healthy volunteers as well as a deep molecular and metabolic characterization of these isolated strains. These F. prausnitzii strains were classified in two phylogroups and three clusters according to 16S rRNA sequences and results support that they would belong to two different genomospecies or genomovars as no genome sequencing has been performed in this work. Differences in enzymes production, antibiotic resistance and immunomodulatory properties were found to be strain-dependent. So far, all F. prausnitzii isolates share some characteristic such as (i) the lack of epithelial cells adhesion, plasmids, anti-microbial, and hemolytic activity and (ii) the presence of DNAse activity. Furthermore, Short Chain Fatty Acids (SCFA) production was assessed for the novel isolates as these products influence intestinal homeostasis. Indeed, the butyrate production has been correlated to the capacity to induce IL-10, an anti-inflammatory cytokine, in peripheral blood mononuclear cells (PBMC) but not to the ability to block IL-8 secretion in TNF-α-stimulated HT-29 cells, reinforcing the hypothesis of a complex anti-inflammatory pathway driven by F. prausnitzii. Altogether, our results suggest that some F. prausnitzii strains could represent good candidates as next-generation probiotic.

The Central Nervous System and the Gut Microbiome

Neurodevelopment is a complex process governed by both intrinsic and extrinsic signals. While historically studied by researching the brain, inputs from the periphery impact many neurological conditions. Indeed, emerging data suggest communication between the gut and the brain in anxiety, depression, cognition, and autism spectrum disorder (ASD). The development of a healthy, functional brain depends on key pre- and post-natal events that integrate environmental cues, such as molecular signals from the gut. These cues largely originate from the microbiome, the consortium of symbiotic bacteria that reside within all animals. Research over the past few years reveals that the gut microbiome plays a role in basic neurogenerative processes such as the formation of the blood-brain barrier, myelination, neurogenesis, and microglia maturation and also modulates many aspects of animal behavior. Herein, we discuss the biological intersection of neurodevelopment and the microbiome and explore the hypothesis that gut bacteria are integral contributors to development and function of the nervous system and to the balance between mental health and disease.

The gut microbiome composition associates with bipolar disorder and illness severity

The gut microbiome is emerging as an important factor in regulating mental health yet it remains unclear what the target should be for psychiatric treatment. We aimed to elucidate the complement of the gut-microbiome community for individuals with bipolar disorder relative to controls; and test for relationships with burden of disease measures. We compared the stool microbiome from individuals with bipolar disorder (n = 115) and control subjects (n = 64) using 16S ribosomal RNA (rRNA) gene sequence analysis. Analysis of molecular variance (AMOVA) revealed global community case-control differences (AMOVA p = 0.047). Operational Taxonomical Unit (OTU) level analysis revealed significantly decreased fractional representation (p < 0.001) of Faecalibacterium after adjustment for age, sex, BMI and false discovery rate (FDR) correction at the p < 0.05 level. Within individuals with bipolar disorder, the fractional representation of Faecalibacterium associated with better self-reported health outcomes based on the Short Form Health Survey (SF12); the Patient Health Questionnaire (PHQ9); the Pittsburg Sleep Quality Index (PSQI); the Generalized Anxiety Disorder scale (GAD7); and the Altman Mania Rating Scale (ASRM), independent of covariates. This study provides the first detailed analysis of the gut microbiome relationships with multiple psychiatric domains from a bipolar population. The data support the hypothesis that targeting the microbiome may be an effective treatment paradigm for bipolar disorder.

The Effect of Bifidobacterium animalis ssp. lactis HN019 on Cellular Immune Function in Healthy Elderly Subjects: Systematic Review and Meta-Analysis

Elderly people have increased susceptibility to infections and cancer that are associated with decline in cellular immune function. The objective of this work was to determine the efficacy of Bifidobacterium (B.) animalis ssp. lactis HN019 (HN019) supplementation on cellular immune activity in healthy elderly subjects. We conducted a systematic review of Medline and Embase for controlled trials that reported polymorphonuclear (PMN) cell phagocytic capacity or natural killer (NK) cell tumoricidal activity following B. lactis HN019 consumption in the elderly. A random effects meta-analysis was performed with standardized mean difference (SMD) and 95% confidence interval between probiotic and control groups for each outcome. A total of four clinical trials were included in this analysis. B. lactis HN019 supplementation was highly efficacious in increasing PMN phagocytic capacity with an SMD of 0.74 (95% confidence interval: 0.38 to 1.11, p < 0.001) and moderately efficacious in increasing NK cell tumoricidal activity with an SMD of 0.43 (95% confidence interval: 0.08 to 0.78, p = 0.02). The main limitations of this research were the small number of included studies, short-term follow-up, and assessment of a single probiotic strain. In conclusion, daily consumption of B. lactis HN019 enhances NK cell and PMN function in healthy elderly adults.

Gut Bifidobacteria Populations in Human Health and Aging

The intestinal microbiota has increasingly been shown to have a vital role in various aspects of human health. Indeed, several studies have linked alterations in the gut microbiota with the development of different diseases. Among the vast gut bacterial community, Bifidobacterium is a genus which dominates the intestine of healthy breast-fed infants whereas in adulthood the levels are lower but relatively stable. The presence of different species of bifidobacteria changes with age, from childhood to old age. Bifidobacterium longum, B. breve, and B. bifidum are generally dominant in infants, whereas B. catenulatum, B. adolescentis and, as well as B. longum are more prevalent in adults. Increasingly, evidence is accumulating which shows beneficial effects of supplementation with bifidobacteria for the improvement of human health conditions ranging from protection against infection to different extra- and intra-intestinal positive effects. Moreover, bifidobacteria have been associated with the production of a number of potentially health promoting metabolites including short chain fatty acids, conjugated linoleic acid and bacteriocins. The aim of this mini-review is to describe the bifidobacteria compositional changes associated with different stages in life, highlighting their beneficial role, as well as their presence or absence in many disease states.

Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection

Alteration of the gut microbial community structure and function through antibiotic use increases susceptibility to colonization by Clostridium difficile and other enteric pathogens. However, the mechanisms that mediate colonization resistance remain elusive. As the leading definable cause of infectious diarrhea, toxigenic C. difficile represents a burden for patients and health care systems, underscoring the need for better diagnostics and treatment strategies. Next-generation sequence data has increased our understanding of how the gut microbiota is influenced by many factors including diet, disease, aging and drugs. However, a microbial-based biomarker differentiating C. difficile infection from antibiotic-associated diarrhea has not been identified. Metabolomics profiling, which is highly responsive to changes in physiological conditions, have shown promise in differentiating subtle disease phenotypes that exhibit a nearly identical microbiome community structure, suggesting metabolite-based biomarkers may be an ideal diagnostic for identifying patients with CDI. This review focuses on the current understanding of structural and functional changes to the gut microbiota during C. difficile infection obtained from studies assessing the microbiome and metabolome of samples from patients and murine models.

Gastrointestinal Microbiota and Their Contribution to Healthy Aging

Studies on populations at different ages have shown that after birth, the gastrointestinal (GI) microbiota composition keeps evolving, and this seems to occur especially in old age. Significant changes in GI microbiota composition in older subjects have been reported in relation to diet, drug use and the settings where the older subjects are living, that is, in community nursing homes or in a hospital. Moreover, changes in microbiota composition in the old age have been related to immunosenescence and inflammatory processes that are pathophysiological mechanisms involved in the pathways of frailty. Frailty is an age-related condition of increased vulnerability to stresses due to the impairment in multiple inter-related physiologic systems that are associated with an increased risk of adverse outcomes, such as falls, delirium, institutionalization, hospitalization and death. Preliminary data suggest that changes in microbiota composition may contribute to the variations in the biological, clinical, functional and psycho-social domains that occur in the frail older subjects. Multidimensional evaluation tools based on a Comprehensive Geriatric Assessment (CGA) have demonstrated to be useful in identifying and measuring the severity of frailty in older subjects. Thus, a CGA approach should be used more widely in clinical practice to evaluate the multidimensional effects potentially related to GI microbiota composition of the older subjects. Probiotics have been shown to be effective in restoring the microbiota changes of older subjects, promoting different aspects of health in elderly people as improving immune function and reducing inflammation. Whether modulation of GI microbiota composition, with multi-targeted interventions, could have an effect on the prevention of frailty remains to be further investigated in the perspective of improving the health status of frail 'high risk' older individuals.

Nutritional advice for community patients: insights from a panel discussion

This article describes the conclusions of an expert panel that discussed four case studies; these were examples of patients typically encountered by nurses working in the community. The panel considered the nutritional and lifestyle advice that could be given by nurses relating to conditions such as irritable bowel syndrome (IBS), depression, chronic fatigue syndrome, vulnerability to common infections, elderly care, recurrent urinary tract infection, antibiotic use, and risk of type 2 diabetes. A general conclusion was the importance of motivational interviewing techniques in achieving full understanding of patients' concerns and to determine the best health strategy. As well as specific guidance appropriate for each disorder, a range of information sources for both health professionals and patients are listed in the paper. The panel noted that, although general nutritional advice can be given by nurses working at GP surgeries and in the community, patients should always be referred to registered dietitians or nutritionists if significant dietary changes are considered.

Whole genome sequencing of "Faecalibaculum rodentium" ALO17, isolated from C57BL/6J laboratory mouse feces

Background

Intestinal microorganisms affect host physiology, including ageing. Given the difficulty in controlling for human studies of the gut microbiome, mouse models provide an alternative avenue to study such relationships. In this study, we report on the complete genome of “Faecalibaculum rodentium” ALO17, a bacterium that was isolated from the faeces of a 9-month-old female C57BL/6J mouse. This strain will be utilized in future in vivo studies detailing the relationships between the gut microbiome and ageing.

Results

The whole genome sequence of “F. rodentium” ALO17 was obtained using single-molecule, real-time (SMRT) technique on a PacBio instrument. The assembled genome consisted of 2,542,486 base pairs of double-stranded DNA with a GC content of 54.0 % and no plasmids. The genome was predicted to contain 2794 open reading frames, 55 tRNA genes, and 38 rRNA genes. The 16S rRNA gene of ALO17 was 86.9 % similar to that of Allobaculum stercoricanis DSM 13633^T, and the average overall nucleotide identity between strains ALO17 and DSM 13633^T was 66.8 %. After confirming the phylogenetic relationship between “F. rodentium” ALO17 and A. stercoricanis DSM 13633^T, their whole genome sequences were compared, revealing that “F. rodentium” ALO17 contains more fermentation-related genes than A. stercoricanis DSM 13633^T. Furthermore, “F. rodentium” ALO17 produces higher levels of lactic acid than A. stercoricanis DSM 13633^T as determined by high-performance liquid chromatography.

Conclusion

The availability of the “F. rodentium” ALO17 whole genome sequence will enhance studies concerning the gut microbiota and host physiology, especially when investigating the molecular relationships between gut microbiota and ageing.

The Microbiome and Musculoskeletal Conditions of Aging: A Review of Evidence for Impact and Potential Therapeutics

Recently, we have begun to realize that the billions of microorganisms living in symbiosis with us have an influence on disease. Evidence is mounting that the alimentary tract microbiome, in particular, influences both host metabolic potential and its innate and adaptive immune system. Inflammatory states characterize many bone and joint diseases of aging. This prompts the hypothesis that the gut microbiome could alter the inflammatory state of the individual and directly influence the development of these common and burdensome clinical problems. Because the microbiome is easily modifiable, this could have major therapeutic impact. This perspective discusses evidence to date on the role of the microbiome and the highly prevalent age-related disorders of osteoporosis, osteoarthritis, gout, rheumatoid arthritis, sarcopenia, and frailty. It also reviews data on the effects of probiotics and prebiotic interventions in animal and human models. Despite suggestive findings, research to date is not conclusive, and we identify priorities for research to substantiate and translate findings.

Signatures of early frailty in the gut microbiota

BACKGROUND

Frailty is arguably the biggest problem associated with population ageing, and associates with gut microbiome composition in elderly and care-dependent individuals. Here we characterize frailty associations with the gut microbiota in a younger community dwelling population, to identify targets for intervention to encourage healthy ageing.

METHOD

We analysed 16S rRNA gene sequence data derived from faecal samples obtained from 728 female twins. Frailty was quantified using a frailty index (FI). Mixed effects models were used to identify associations with diversity, operational taxonomic units (OTUs) and taxa. OTU associations were replicated in the Eldermet cohort. Phenotypes were correlated with modules of OTUs collapsed by co-occurrence.

RESULTS

Frailty negatively associated with alpha diversity of the gut microbiota. Models considering a number of covariates identified 637 OTUs associated with FI. Twenty-two OTU associations were significant independent of alpha diversity. Species more abundant with frailty included Eubacterium dolichum and Eggerthella lenta. A Faecalibacterium prausnitzii OTU was less abundant in frailer individuals, and retained significance in discordant twin analysis. Sixty OTU associations were replicated in the Eldermet cohort. OTU co-occurrence modules had mutually exclusive associations between frailty and alpha diversity.

CONCLUSIONS

There was a striking negative association between frailty and gut microbiota diversity, underpinned by specific taxonomic associations. Whether these relationships are causal or consequential is unknown. Nevertheless, they represent targets for diagnostic surveillance, or for intervention studies to improve vitality in ageing.

Gut Microbiome: What We Do and Don't Know

Within the last decade, research regarding the human gut microbiome has exploded. While the gastrointestinal tract was once regarded simply as a digestive organ, new technologies have led the science world to wonder about the impact that the gut microbiota may have on human health and disease. The gut microbiome is now becoming known for its role in metabolism, immune defense, and behavior. From in utero variations to those that rapidly occur post partum, our gut microbiome changes with age, environment, stress, diet, and health status as well as medication exposure. This article reviews what is currently known regarding various influences on the gut microbiome and is meant to encourage the reader to further explore the unknown.

The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities

Increasing evidence points to a role of altered microbiota on inflammation, obesity, and other chronic conditions. This commentary addresses the connection between osteosarcopenic obesity syndrome, an impairment in bone, muscle, and adipose tissues that occurs concurrently, with the altered microbiota in elderly individuals, particularly those living in long-term care facilities. As elderly move to long-term care facilities, they experience changes in gut bacteria that might exasperate the underlying conditions such as osteosarcopenic obesity. These individuals have exponentially higher osteoporotic fracture rates and immobility impairments compared to independently living individuals. However, there is very limited research on this topic and more insight is needed on the impact of probiotic treatment and diet in older individuals, especially those with chronic conditions related to aging, such as osteosarcopenic obesity.

Improving healthspan via changes in gut microbiota and fermentation

Dietary resistant starch impact on intestinal microbiome and improving healthspan is the topic of this review. In the elderly population, dietary fiber intake is lower than recommended. Dietary resistant starch as a source of fiber produces a profound change in gut microbiota and fermentation in animal models of aging. Dietary resistant starch has the potential for improving healthspan in the elderly through multiple mechanisms as follows: (1) enhancing gut microbiota profile and production of short-chain fatty acids, (2) improving gut barrier function, (3) increasing gut peptides that are important in glucose homeostasis and lipid metabolism, and (4) mimicking many of the effects of caloric restriction including upregulation of genes involved in xenobiotic metabolism.

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality

Alterations in the composition of the intestinal microbiota have been correlated with aging and measures of frailty in the elderly. However, the relationships between microbial dynamics, age-related changes in intestinal physiology, and organismal health remain poorly understood. Here, we show that dysbiosis of the intestinal microbiota, characterized by an expansion of the Gammaproteobacteria, is tightly linked to age-onset intestinal barrier dysfunction in Drosophila. Indeed, alterations in the microbiota precede and predict the onset of intestinal barrier dysfunction in aged flies. Changes in microbial composition occurring prior to intestinal barrier dysfunction contribute to changes in excretory function and immune gene activation in the aging intestine. In addition, we show that a distinct shift in microbiota composition follows intestinal barrier dysfunction, leading to systemic immune activation and organismal death. Our results indicate that alterations in microbiota dynamics could contribute to and also predict varying rates of health decline during aging in mammals.

Improving the bowel habits of elderly residents in a nursing home using probiotic fermented milk

Our aim was to determine whether a fermented milk drink containing probiotics could improve the bowel habits of frail elderly individuals living in a nursing home. A total of 135 participants were enrolled in this pilot study. The bowel habits (stool quality and bowel movements) were recorded by nursing staff during a baseline period of 3 weeks. After this period participants received daily a fermented milk drink containing minimally 6.5×109 colony forming units of Lactobacillus casei Shirota (LcS) for 6 weeks. During this period, bowel habits were recorded and compared to baseline period. Forty-four participants (74-99 years old) were compliant and used for analysis. Consumption of fermented milk containing LcS significantly increased the percentage of ideal stool types per week (P<0.01), lowered the percentage of constipation stool types per week (P<0.01) and significantly lowered the percentage of diarrhoea stool types per week (P=0.016) as compared to the baseline period. The study product had no significant effect on bowel movements. During the study, no changes in laxative usage or adverse events associated with the study product were reported. Our results suggest that a fermented milk containing LcS significantly improves the bowel habits of frail elderly residents in a nursing home. These promising results should be further substantiated by a confirmatory study.

Colonic bacterial composition in Parkinson's disease

INTRODUCTION

We showed that Parkinson's disease (PD) patients have alpha-synuclein (α-Syn) aggregation in their colon with evidence of colonic inflammation. If PD patients have altered colonic microbiota, dysbiosis might be the mechanism of neuroinflammation that leads to α-Syn misfolding and PD pathology.

METHODS

Sixty-six sigmoid mucosal biopsies and 65 fecal samples were collected from 38 PD patients and 34 healthy controls. Mucosal-associated and feces microbiota compositions were characterized using high-throughput ribosomal RNA gene amplicon sequencing. Data were correlated with clinical measures of PD, and a predictive assessment of microbial community functional potential was used to identify microbial functions.

RESULTS

The mucosal and fecal microbial community of PD patients was significantly different than control subjects, with the fecal samples showing more marked differences than the sigmoid mucosa. At the taxonomic level of genus, putative, "anti-inflammatory" butyrate-producing bacteria from the genera Blautia, Coprococcus, and Roseburia were significantly more abundant in feces of controls than PD patients. Bacteria from the genus Faecalibacterium were significantly more abundant in the mucosa of controls than PD. Putative, "proinflammatory" Proteobacteria of the genus Ralstonia were significantly more abundant in mucosa of PD than controls. Predictive metagenomics indicated that a large number of genes involved in metabolism were significantly lower in the PD fecal microbiome, whereas genes involved in lipopolysaccharide biosynthesis and type III bacterial secretion systems were significantly higher in PD patients.

CONCLUSION

This report provides evidence that proinflammatory dysbiosis is present in PD patients and could trigger inflammation-induced misfolding of α-Syn and development of PD pathology.

Composition and temporal stability of the gut microbiota in older persons

The composition and function of the human gut microbiota has been linked to health and disease. We previously identified correlations between habitual diet, microbiota composition gradients and health gradients in an unstratified cohort of 178 elderly subjects. To refine our understanding of diet–microbiota associations and differential taxon abundance, we adapted an iterative bi-clustering algorithm (iterative binary bclustering of gene sets (iBBiG)) and applied it to microbiota composition data from 732 faecal samples from 371 ELDERMET cohort subjects, including longitudinal samples. We thus identified distinctive microbiota configurations associated with ageing in both community and long-stay residential care elderly subjects. Mixed-taxa populations were identified that had clinically distinct associations. Microbiota temporal instability was observed in both community-dwelling and long-term care subjects, particularly in those with low initial microbiota diversity. However, the stability of the microbiota of subjects had little impact on the directional change of the microbiota as observed for long-stay subjects who display a gradual shift away from their initial microbiota. This was not observed in community-dwelling subjects. This directional change was associated with duration in long-stay. Changes in these bacterial populations represent the loss of the health-associated and youth-associated microbiota components and gain of an elderly associated microbiota. Interestingly, community-associated microbiota configurations were impacted more by the use of antibiotics than the microbiota of individuals in long-term care, as the community-associated microbiota showed more loss but also more recovery following antibiotic treatment. This improved definition of gut microbiota composition patterns in the elderly will better inform the design of dietary or antibiotic interventions targeting the gut microbiota.

Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort

Background

The incidence of esophageal adenocarcinoma (EAC) has increased nearly five-fold over the last four decades in the United States. Barrett’s esophagus, the replacement of the normal squamous epithelial lining with a mucus-secreting columnar epithelium, is the only known precursor to EAC. Like other parts of the gastrointestinal (GI) tract, the esophagus hosts a variety of bacteria and comparisons among published studies suggest bacterial communities in the stomach and esophagus differ. Chronic infection with Helicobacter pylori in the stomach has been inversely associated with development of EAC, but the mechanisms underlying this association remain unclear.

Methodology

The bacterial composition in the upper GI tract was characterized in a subset of participants (n=12) of the Seattle Barrett’s Esophagus Research cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples collected from squamous esophagus, Barrett’s esophagus, stomach corpus and stomach antrum. Three of the individuals were sampled at two separate time points. Prevalence of H. pylori infection and subsequent development of aneuploidy (n=339) and EAC (n=433) was examined in a larger subset of this cohort.

Results/Significance

Within individuals, bacterial communities of the stomach and esophagus showed overlapping community membership. Despite closer proximity, the stomach antrum and corpus communities were less similar than the antrum and esophageal samples. Re-sampling of study participants revealed similar upper GI community membership in two of three cases. In this Barrett’s esophagus cohort, Streptococcus and Prevotella species dominate the upper GI and the ratio of these two species is associated with waist-to-hip ratio and hiatal hernia length, two known EAC risk factors in Barrett’s esophagus. H. pylori-positive individuals had a significantly decreased incidence of aneuploidy and a non-significant trend toward lower incidence of EAC.

Inflammatory bowel disease and the elderly: a review

Inflammatory bowel disease among the elderly is common, with growing incident and prevalence rates. Compared with younger IBD patients, genetics contribute less to the pathogenesis of older-onset IBD, with dysbiosis and dysregulation of the immune system playing a more significant role. Diagnosis may be difficult in older individuals, as multiple other common diseases can mimic IBD in this population. The clinical manifestations in older-onset IBD are distinct, and patients tend to have less of a disease trajectory. Despite multiple effective medical and surgical treatment strategies for adults with Crohn's disease and ulcerative colitis, efficacy studies typically have excluded older subjects. A rapidly ageing population and increasing rates of Crohn's and ulcerative colitis make the paucity of data in older adults with IBD an increasingly important clinical issue.

Diversity of Intestinal Clostridium coccoides Group in the Japanese Population, as Demonstrated by Reverse Transcription-Quantitative PCR

We used sensitive rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) to quantify the Clostridium coccoides group, which is a major anaerobic population in the human intestine. For this purpose, the C. coccoides group was classified into 3 subgroups and 19 species for expediency in accordance with the existing database, and specific primers were newly developed to evaluate them. Population levels of the C. coccoides group in human feces determined by RT-qPCR were equivalent to those determined by fluorescence in situ hybridization. RT-qPCR analysis of fecal samples from 96 volunteers (32 young children, 32 adults and 32 elderly) by using the 22 new primer sets together with the C. coccoides group-specific primer setm revealed that (i) total counts obtained as the sum of the 3 subgroups and 19 species were equivalent to the results obtained by using the C. coccoides group-specific primer set; (ii) total C. coccoides-group counts in the elderly were significantly lower than those in young children and adults; (iii) genus Blautia was the most common subgroup in the human intestinal C. coccoides-group populations at all age populations tested; (iv) the prevalences of Fusicatenibacter saccharivorans and genus Dorea were significantly higher in adults than in young children and the elderly; and (v) the prevalences of C. scindens and C. hylemonae, both of which produce secondary bile acid in the human intestine, were significantly higher in the elderly than in young children and adults. Hierarchical clustering and principal component analysis showed clear separation of the bacterial components between adult and elderly populations. Taken together, these data suggest that aging plays an important role in the diversity of C. coccoides-group populations in human intestinal microbiota; changes in this diversity likely influence the health of the host.

Understanding gut microbiota in elderly's health will enable intervention through probiotics

Today, advances in the public health system of most countries have managed to extend notably life expectancy, however, elderly's health remain as a very serious concern. The lifelong stimulation of innate and adaptive immune systems leads to immunosenescence and, as result, to a low ability to produce immunoglobulins against pathogens but also to a low-grade chronic inflammatory state (inflammaging) that is linked to most age-related health problems, such as dementia, Alzheimer or atherosclerosis. This inflammatory state could make the host more sensitive to intestinal microbes, or vice versa, as changes in the gut microbiota composition are related to the progression of diseases and frailty in the elderly population. It was considered that gut microbiota changed during aging, with an increase of Bacteroidetes vs. Firmicutes proportion and a reduction of bifidobacterial counts, however recent studies reported a great inter-individual variation among elderly and a significant relationship between gut microbiota, diet and institution or community living. Intervention studies of probiotics and prebiotics in elderly are not very abundant, but most cases showed that Bifidobacterium populations can efficiently be stimulated with a concomitant decrease of Enterobacteria. Furthermore, also some studies demonstrated that probiotics decreased the synthesis of pro-inflammatory cytokines which are upregulated in the elderly, such as interleukin (IL)-8, IL-6 or tumour necrosis factor ?, among others, and they increased the levels of activated lymphocytes, natural killer cells, phagocytic activity and even showed a greater response to influenza vaccination. This suggests that direct manipulation of the gut microbiota may improve adaptive immune response and reduce inflammatory secretions, therefore compensating immunosenescence effects, however, there are no records of their effect on clinical symptoms or risk for disease. Those facts reveal that this is an open research field with very good scientific perspectives and above all they could bring likely improvements in the wellbeing of our seniors.

Review on microbiota and effectiveness of probiotics use in older

The aim of the present systematic review is to summarize the existing knowledge about the human microbiota in the elderly and the effects of probiotics in elderly population. The elderly subjects, compared to adult population, show a reduction in the diversity of the microbiota, characterized by a large interindividual variability, with lower numbers of Firmicutes, Bifidobacteria, Clostridium cluster XIV, Faecalibacterium Prausnitzii, Blautia coccoides-Eubacterium rectal and higher presence of Enterobacteriaceae and Bacteroidetes. These differences of the intestinal microbiota of the elderly may not necessarily be caused by aging, but they could be associated with the decline of the general state of health with malnutrition and with increased need for medication, such as antibiotics and nonsteroidal anti-inflammatory drugs, situations that occur frequently in the elderly. Differences have been demonstrated in the composition of the microbiota between healthy elderly subjects and hospitalized or institutionalized elderly subjects. These findings which further indicates that the living conditions, health status, nutrition and drugs have a significant effect on the composition of the microbiota. According to the available knowledge, the use of probiotics is safe and could represent an useful intervention to prevent or treat antibiotic-associated diarrhea, in addition to reducing the severity of symptoms, other than to help the management of constipation.

Microbial shifts in the aging mouse gut

BACKGROUND

The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these results may be confounded by other variables that often change with age such as diet and place of residence. To test these associations in a more controlled model system, we examined the relationship between age, frailty, and the gut microbiome of female C57BL/6 J mice.

RESULTS

The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family, which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and older mice. The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis, and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting, was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded β-glucuronidases, which can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on gut homeostasis.

CONCLUSION

We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty. Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors.

Compositional dynamics of the human intestinal microbiota with aging: implications for health

The human gut contains trillions of microbes which form an essential part of the complex ecosystem of the host. This microbiota is relatively stable throughout adult life, but may fluctuate over time with aging and disease. The gut microbiota serves a number of functions including roles in energy provision, nutrition and also in the maintenance of host health such as protection against pathogens. This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. Understanding the composition and function of the gut microbiota along with the changes it undergoes overtime should aid the design of novel therapeutic strategies to counteract such alterations. These strategies include probiotic and prebiotic preparations as well as targeted nutrients, designed to enrich the gut microbiota of the aging population.

Compositional dynamics of the human intestinal microbiota with aging: implications for health

The human gut contains trillions of microbes which form an essential part of the complex ecosystem of the host. This microbiota is relatively stable throughout adult life, but may fluctuate over time with aging and disease. The gut microbiota serves a number of functions including roles in energy provision, nutrition and also in the maintenance of host health such as protection against pathogens. This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. Understanding the composition and function of the gut microbiota along with the changes it undergoes overtime should aid the design of novel therapeutic strategies to counteract such alterations. These strategies include probiotic and prebiotic preparations as well as targeted nutrients, designed to enrich the gut microbiota of the aging population.

Faecal microbiota of cats with insulin-treated diabetes mellitus

Microorganisms within the gastrointestinal tract significantly influence metabolic processes within their mammalian host, and recently several groups have sought to characterise the gastrointestinal microbiota of individuals affected by metabolic disease. Differences in the composition of the gastrointestinal microbiota have been reported in mouse models of type 2 diabetes mellitus, as well as in human patients. Diabetes mellitus in cats has many similarities to type 2 diabetes in humans. No studies of the gastrointestinal microbiota of diabetic cats have been previously published. The objectives of this study were to compare the composition of the faecal microbiota of diabetic and non-diabetic cats, and secondarily to determine if host signalment and dietary factors influence the composition of the faecal microbiota in cats. Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. ANOSIM based on the unweighted UniFrac distance metric identified no difference in the composition of the faecal microbiota between diabetic and non-diabetic cats, and no significant differences in the proportions of dominant bacteria by phylum, class, order, family or genus as determined by 16S rRNA gene sequencing were identified between diabetic and non-diabetic cats. qPCR identified a decrease in Faecalibacterium spp. in cats aged over ten years. Cat breed or gender, dietary carbohydrate, protein or fat content, and dietary formulation (wet versus dry food) did not affect the composition of the faecal microbiota. In conclusion, the composition of the faecal microbiota was not altered by the presence of diabetes mellitus in cats. Additional studies that compare the functional products of the microbiota in diabetic and non-diabetic cats are warranted to further investigate the potential impact of the gastrointestinal microbiota on metabolic diseases such as diabetes mellitus in cats.

Diet and the development of the human intestinal microbiome

The important role of the gut microbiome in maintaining human health has necessitated a better understanding of the temporal dynamics of intestinal microbial communities as well as the host and environmental factors driving these dynamics. Genetics, mode of birth, infant feeding patterns, antibiotic usage, sanitary living conditions and long term dietary habits contribute to shaping the composition of the gut microbiome. This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly. The infant gut microbiota is characterized by a high degree of instability, only reaching a state similar to that of adults by 2–3 years of age; consistent with the establishment of a varied solid food diet. The diet-related factors influencing the development of the infant gut microbiome include whether the child is breast or formula-fed as well as how and when solid foods are introduced. In contrast to the infant gut, the adult gut microbiome is resilient to large shifts in community structure. Several studies have shown that dietary changes induce transient fluctuations in the adult microbiome, sometimes in as little as 24 h; however, the microbial community rapidly returns to its stable state. Current knowledge of how long-term dietary habits shape the gut microbiome is limited by the lack of long-term feeding studies coupled with temporal gut microbiota characterization. However, long-term weight loss studies have been shown to alter the ratio of the Bacteroidetes and Firmicutes, the two major bacterial phyla residing in the human gastrointestinal tract. With aging, diet-related factors such as malnutrition are associated with microbiome shifts, although the cause and effect relationship between these factors has not been established. Increased pharmaceutical usage is also more prevalent in the elderly and can contribute to reduced gut microbiota stability and diversity. Foods containing prebiotic oligosaccharide components that nurture beneficial commensals in the gut community and probiotic supplements are being explored as interventions to manipulate the gut microbiome, potentially improving health status.

Gut microbiota in older subjects: variation, health consequences and dietary intervention prospects

Alterations in intestinal microbiota composition and function have been linked to conditions including functional gastrointestinal disorders, obesity and diabetes. The gut microbiome encodes metabolic capability in excess of that encoded by the human genome, and bacterially produced enzymes are important for releasing nutrients from complex dietary ingredients. Previous culture-based studies had indicated that the gut microbiota of older people was different from that of younger adults, but the detailed findings were contradictory. Small-scale studies had also shown that the microbiota composition could be altered by dietary intervention or supplementation. We showed that the core microbiota and aggregate composition in 161 seniors was distinct from that of younger persons. To further investigate the reasons for this variation, we analysed the microbiota composition of 178 elderly subjects for whom the dietary intake data were available. The data revealed distinct microbiota composition groups, which overlapped with distinct dietary patterns that were governed by where people lived: at home, in rehabilitation or in long-term residential care. These diet-microbiota separations correlated with cluster analysis of NMR-derived faecal metabolites and shotgun metagenomic data. Major separations in the microbiota correlated with selected clinical measurements. It should thus be possible to programme the microbiota to enrich bacterial species and activities that promote healthier ageing. A number of other studies have investigated the effect of certain dietary components and their ability to modulate the microbiota composition to promote health. This review will discuss dietary interventions conducted thus far, especially those in elderly populations and highlight their impact on the intestinal microbiota.

Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii

Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer.

Maintenance of a healthy trajectory of the intestinal microbiome during aging: a dietary approach

Sharing an intense transgenomic metabolism with the host, the intestinal microbiota is an essential factor for several aspects of the human physiology. However, several age-related factors, such as changes diet, lifestyle, inflammation and frailty, force the deterioration of this intestinal microbiota-host mutualistic interaction, compromising the possibility to reach longevity. In this scenario, the NU-AGE project involves the development of dietary interventions specifically tailored to the maintenance of a healthy trajectory of the intestinal microbiome, counteracting all processes connected to the pathophysiology of the human aging.

Role of the gut microbiota in human nutrition and metabolism

The human gastrointestinal tract harbors trillions of bacteria, most of which are commensal and have adapted over time to the milieu of the human colon. Their many metabolic interactions with each other, and with the human host, influence human nutrition and metabolism in diverse ways. Our understanding of these influences has come through breakthroughs in the molecular profiling of the phylogeny and the metabolic capacities of the microbiota. The gut microbiota produce a variety of nutrients including short-chain fatty acids, B vitamins, and vitamin K. Because of their ability to interact with receptors on epithelial cells and subepithelial cells, the microbiota also release a number of cellular factors that influence human metabolism. Thus, they have potential roles in the pathogenesis of metabolic syndrome, diabetes, non-alcoholic fatty liver disease, and cognition, which extend well beyond their traditional contribution to nutrition. This review explores the roles of the gut microbiota in human nutrition and metabolism, and the putative mechanisms underlying these effects.

Effects of three-month intake of synbiotic on inflammation and body composition in the elderly: a pilot study

We hypothesize that improvements in the gut microbiota are capable of ameliorating gut permeability and, consequently, reducing systemic inflammation and the risk of frailty. This study aims to evaluate some effects of synbiotic supplementation on inflammatory markers and the body composition of the elderly at risk of frailty. In a double-blind study that lasted three months, 17 elderly individuals fulfilling one frailty criteria (grip strength) were randomly distributed into two groups: SYN (n = 9), daily intake of synbiotic (6 g Frutooligossacarides, 108 to 109 CFU Lactobacillus paracasei, 108 to 109 CFU Lactobacillus rhamnosus, 108 to 109 CFU Lactobacillus acidophilus and 108 to 109 CFU Bifidobacterium lactis), or placebo (maltodextrin; PLA; n = 8). Subjects were analyzed for anthropometric measurements, bioelectric impedance with vectorial analysis (BIVA), IL-6 and TNF-α. A comparison between groups did not show any difference for the variables investigated. In turn, individual analysis of electrical impedance (BIVA) demonstrated that the majority of SYN individuals maintained or improved their tissue hydration, when compared to the PLA group after supplementation. In conclusion, three months of synbiotic supplementation did not promote any significant changes in inflammatory cytokines or body composition, but demonstrated a trend towards a preservation of hydration status in apparently healthy elderly individuals.

Microbiota and healthy ageing: observational and nutritional intervention studies

Hundred years ago Metchnikoff associated human health and particularly healthy ageing with a specific type of gut microbiota. Classical culture methods associated a decrease in bifidobacteria and an increase in enterobacteria with ageing. Modern molecular methods blurred this simple picture and documented a substantial inter-individual variability for the gut microbiome even when stratifying the elderly subjects according to health status. Nutritional interventions with resistant starch showed consistent gut microbiota changes across studies from different geographical areas and prebiotic supplementation induced a 10-fold increase in gut bifidobacteria. However, in the ELDERMET study, microbiota changes do not precede, but follow the changes in health status of elderly subjects possibly as a consequence of diet changes.

Probiotics and prebiotics and health in ageing populations

In healthy adults microbial communities that colonise different regions of the human colon contribute nutrients and energy to the host via the fermentation of non-digestible dietary components in the large intestine. A delicate balance of microbial species is required to maintain healthy metabolism and immune function. Disturbance in this microbial balance can have negative consequences for health resulting in elevated inflammation and infection, that are contributory factors in diabetes and cancer. There is a growing awareness that the microbial balance in the colon may become increasingly perturbed with aging and therefore hasten the onset of certain diseases. Societal and dietary factors influence microbial community composition both in the short and long term in the elderly (>65 years old) whilst immunosenescence may also be linked to a perturbed distal gut microbiota and frailty in the elderly. Significant progress has been made in defining some of the dominant members of the microbial community in the healthy large intestine and in identifying their roles in metabolism. There is therefore an urgent need for better awareness of the impact of diet, prebiotic and probiotic strategies in driving human colonic microbial composition in order to understand the possibilities for maintaining healthy gut function and well-being in an increasingly elderly population. Here we review gut microbial changes associated with aging and how diet, prebiotics and probiotics may modulate the gut microbiota to maintain health in the elderly.

Ageing and gut microbes: perspectives for health maintenance and longevity

The ageing process affects the human gut microbiota phylogenetic composition and its interaction with the immune system. Age-related gut microbiota modifications are associated with immunosenescence and inflamm-ageing in a sort of self-sustaining loop, which allows the placement of gut microbiota unbalances among both the causes and the effects of the inflamm-ageing process. Even if, up to now, the link between gut microbiota and the ageing process is only partially understood, the gut ecosystem shows the potential to become a promising target for strategies able to contribute to the health status of older people. In this context, the consumption of pro/prebiotics may be useful in both prevention and treatment of age-related pathophysiological conditions, such as recovery and promotion of immune functions, i.e. adjuvant effect for influenza vaccine, and prevention and/or alleviation of common "winter diseases", as well as constipation and Clostridium difficile-associated diarrhoea. Moreover, being involved in different mechanisms which concur in counteracting inflammation, such as down-regulation of inflammation-associated genes and improvement of colonic mucosa conditions, probiotics have the potentiality to be involved in the promotion of longevity.

The gut microbial metabolome: modulation of cancer risk in obese individuals

Obesity is a critical health concern and although genetic factors may predispose an individual to become obese, changes in diet and lifestyle over the last few decades are likely to be significant contributors. Even so, it has been suggested that the causes of the current obesity crisis are not simply explained by changes in eating and exercise habits. Evidence suggests that the gut microbiota may play an important role in obesity and may be a factor in the development of associated disease including diabetes, CVD, non-alcoholic fatty liver disease and cancer. There have been tremendous advances in knowledge regarding the composition of human gut microbiota, but less is known about their function and role within the human host. It is becoming widely accepted that the products of microbial metabolism influence human health and disease, particularly with respect to immune response and inflammation. However, in most cases, the products of microbial metabolism are uncharacterised and their mechanism of action remains unknown. This review addresses the role of the metabolites produced by gut microbiota in cancer and obesity. It is clear that only if the link between microbial diversity and metabolic functionality is firmly established, will the mechanism by which gut microbiota maintains health or contributes to disease development be elucidated.

Role of the intestinal microbiome in health and disease: from correlation to causation

Recorded observations indicating an association between intestinal microbes and health are long-standing in terms of specific diseases, but emerging high-throughput technologies that characterize microbial communities in the intestinal tract are suggesting new roles for the supposedly normal microbiome. This review considers the nature of the evidence supporting a relationship between the microbiota and the predisposition to disease as associative, correlative, or causal. Altogether, indirect or associative support currently dominates the evidence base, which now suggests that the intestinal microbiome can be linked to a growing number of over 25 diseases or syndromes. While only a handful of cause-and-effect studies have been performed, this form of evidence is increasing. The results of such studies are expected to be useful in monitoring disease development, in providing a basis for personalized treatments, and in indicating future therapeutic avenues.

Gut microbiota composition correlates with diet and health in the elderly

Alterations in intestinal microbiota composition are associated with several chronic conditions, including obesity and inflammatory diseases. The microbiota of older people displays greater inter-individual variation than that of younger adults. Here we show that the faecal microbiota composition from 178 elderly subjects formed groups, correlating with residence location in the community, day-hospital, rehabilitation or in long-term residential care. However, clustering of subjects by diet separated them by the same residence location and microbiota groupings. The separation of microbiota composition significantly correlated with measures of frailty, co-morbidity, nutritional status, markers of inflammation and with metabolites in faecal water. The individual microbiota of people in long-stay care was significantly less diverse than that of community dwellers. Loss of community-associated microbiota correlated with increased frailty. Collectively, the data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.

Aging of the human metaorganism: the microbial counterpart

Human beings have been recently reviewed as 'metaorganisms' as a result of a close symbiotic relationship with the intestinal microbiota. This assumption imposes a more holistic view of the ageing process where dynamics of the interaction between environment, intestinal microbiota and host must be taken into consideration. Age-related physiological changes in the gastrointestinal tract, as well as modification in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbial ecosystem. Here we review the current knowledge of the changes occurring in the gut microbiota of old people, especially in the light of the most recent applications of the modern molecular characterisation techniques. The hypothetical involvement of the age-related gut microbiota unbalances in the inflamm-aging, and immunosenescence processes will also be discussed. Increasing evidence of the importance of the gut microbiota homeostasis for the host health has led to the consideration of medical/nutritional applications of this knowledge through the development of probiotic and prebiotic preparations specific for the aged population. The results of the few intervention trials reporting the use of pro/prebiotics in clinical conditions typical of the elderly will be critically reviewed.

Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth

Faecalibacterium prausnitzii is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of F. prausnitzii strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of F. prausnitzii sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin. Furthermore, F. prausnitzii strains competed successfully in coculture with two other abundant pectin-utilizing species, Bacteroides thetaiotaomicron and Eubacterium eligens, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp. among human colonic anaerobes. Most strains grew on N-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of F. prausnitzii in the colonic community but also suggest factors in the gut environment that may limit its distribution.

Intestinal microbiota in human health and disease: the impact of probiotics

The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis.

Optimising bacterial DNA extraction from faecal samples: comparison of three methods

Culture independent methods are used widely in diagnostic laboratories for infectious disease Isolation of genomic DNA from clinical samples is the first and important step in the procedure. Several procedures for extracting DNA from faecal samples have been described, including different mechanical cell disruptors. To our knowledge, the use of TissueLyser as a mechanical disruptor on faecal samples before DNA extraction has not been previously described. The purpose of the study was to implement a method for preparing faecal samples for optimal DNA extraction. Thus, three different procedures for extracting DNA from human faeces were compared. This was done either by using the mechanical disrupter by Mini BeadBeater 8, or the TissueLyser both followed by DNA purification using QIAamp DNA stool MiniKit, in comparison with DNA extractions using QIAamp DNA stool MiniKit without any prior mechanical disruption, according to manufacturer’s instructions. The obtained DNA from the three procedures was analysed by DGGE, and the number of bands was compared between each procedure. There was no significant difference between the numbers of bacterial bands obtained from DGGE when using a TissueLyser or Mini BeadBeater 8, so the two different mechanical cell disruptors can be used comparably when isolating bacterial DNA from faecal samples. The QIAamp DNA stool MiniKit alone resulted in a reduced number of bands compared to the two mechanical disruption methods.