Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects

Effects of probiotic supplementation on the gut microbiota composition of adults: a systematic review of randomized clinical trials

Researchers have associated the therapeutic potential of probiotics with its ability to modulate gut microbiota, which is considered an "invisible organ" of the human body. The present study investigates the effects of probiotic supplementation on the gut microbiota composition of adults. The authors conducted a systematic review of the literature published in six different databases. The search followed PRISMA guidelines and aimed to identify randomized clinical trials on probiotic supplementation. All relevant publications indexed up to May 28, 2021, were retrieved. Then, the authors defined the inclusion and exclusion criteria. Two independent reviewers performed study screening, data extraction, and quality assessment. A total of 2,404 publications were retrieved, and eight studies met the eligibility criteria. The included randomized clinical trials were published between 2015 to 2020. The worldwide studies included adults aged from 18 to 79 years, most of whom were women (66.5%). Only one of the included studies observed significant effects on fecal microbiota composition in the relative abundance of Bacteroidetes and Firmicutes phyla in comparison with the placebo treatment. Overall, this systematic review could not draw consistent conclusions on the effects of probiotic supplementation on the gut microbiota composition of adults.

Dysbiosis, malnutrition and enhanced gut-lung axis contribute to age-related respiratory diseases

Older people are at an increased risk of developing respiratory diseases such as chronic obstructive pulmonary diseases, asthma, idiopathic pulmonary fibrosis or lung infections. Susceptibility to these diseases is partly due to the intrinsic ageing process, characterized by genomic, cellular and metabolic hallmarks and immunosenescence, and is associated with changes in the intestinal microbiota. Importantly, in the lungs, ageing is also associated with a dysbiosis and loss of resilience of the resident microbiota and alterations of the gut-lung axis. Notably, as malnutrition is often observed in the elderly, nutrition is one of the most accessible modifiable factors affecting both senescence and microbiota. This article reviews the changes affecting the lung and its resident microbiota during ageing, as well as the interconnections between malnutrition, senescence, microbiota, gut-lung axis and respiratory health. As the communication along the gut-lung axis becomes more permissive with ageing, this review also explores the evidence that the gut and lung microbiota are key players in the maintenance of healthy lungs, and as such, are potential targets for nutrition-based preventive strategies against lung disease in elderly populations.

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations

Background

The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.

Results

We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.

Conclusions

Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We’ve proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2623-x) contains supplementary material, which is available to authorized users.

The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations

Background

High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed.

Methods

Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed.

Results

No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples.

Conclusions

Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.

Exploring the influence of the gut microbiota and probiotics on health: a symposium report

The present report describes the presentations delivered at the 7th International Yakult Symposium, ‘The Intestinal Microbiota and Probiotics: Exploiting Their Influence on Health’, in London on 22–23 April 2013. The following two themes associated with health risks were covered: (1) the impact of age and diet on the gut microbiota and (2) the gut microbiota's interaction with the host. The strong influence of the maternal gut microbiota on neonatal colonisation was reported, as well as rapid changes in the gut microbiome of older people who move from community living to residential care. The effects of dietary changes on gut metabolism were described and the potential influence of inter-individual microbiota differences was noted, in particular the presence/absence of keystone species involved in butyrate metabolism. Several speakers highlighted the association between certain metabolic disorders and imbalanced or less diverse microbiota. Data from metagenomic analyses and novel techniques (including an ex vivo human mucosa model) provided new insights into the microbiota's influence on coeliac, obesity-related and inflammatory diseases, as well as the potential of probiotics. Akkermansia muciniphila and Faecalibacterium prausnitzii were suggested as targets for intervention. Host–microbiota interactions were explored in the context of gut barrier function, pathogenic bacteria recognition, and the ability of the immune system to induce either tolerogenic or inflammatory responses. There was speculation that the gut microbiota should be considered a separate organ, and whether analysis of an individual's microbiota could be useful in identifying their disease risk and/or therapy; however, more research is needed into specific diseases, different population groups and microbial interventions including probiotics.

Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type

Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that Methanobrevibacter spp. are the dominant methanogens in the rumen, with Methanobrevibacter smithii being the most abundant species. Differences in the abundance of Methanobrevibacter smithii and Methanosphaera stadtmanae genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of Methanobrevibacter smithii genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals.

Meta-analyses of studies of the human microbiota

Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.

The individual-specific and diverse nature of the preterm infant microbiota

OBJECTIVE

To examine the composition of the evolving microbiota of preterm infants at weeks 2 and 4 of life.

SETTINGS

The paediatric intensive care unit of the Cork University Maternity Hospital.

METHODS

The microbial diversity of faecal samples from 10 preterm infants was determined using 16S rRNA amplicon pyrosequencing technology.

RESULTS

In total, 452 863 sequences were obtained from 20 faecal samples collected from 10 preterm infants, allowing a level of analysis not previously reported. The preterm infant microbiota samples were dominated by Proteobacteria (46%), followed by Firmicutes (45%), while the phyla Actinobacteria (2%) and Bacteroidetes (7%) were detected at much lower levels at week 2 of life. This colonisation pattern was similar at week 4 of life. At the family level, Enterobacteriaceae were detected at 50% and 58% at weeks 2 and 4, respectively. The preterm infants were characterised by a lack of detectable Bifidobacterium and Lactobacillus genera commonly associated with the infant gut. In addition to the dominance of the Proteobacteria, a high level of interindividual variation was observed, indeed the relative proportions of different phyla, families and genera in different infants ranged from <1% to >90%.

CONCLUSIONS

The results indicate that in addition to an uncharacteristic microbiota relative to that reported for healthy term infants, there was a large interindividual variation in the faecal microbiota diversity of preterm infants suggesting that the preterm microbiota is individual-specific and does not display a uniformity among infants.

Microbial-mammalian cometabolites dominate the age-associated urinary metabolic phenotype in Taiwanese and American populations

Understanding the metabolic processes associated with aging is key to developing effective management and treatment strategies for age-related diseases. We investigated the metabolic profiles associated with age in a Taiwanese and an American population. ¹H NMR spectral profiles were generated for urine specimens collected from the Taiwanese Social Environment and Biomarkers of Aging Study (SEBAS; n = 857; age 54-91 years) and the Mid-Life in the USA study (MIDUS II; n = 1148; age 35-86 years). Multivariate and univariate linear projection methods revealed some common age-related characteristics in urinary metabolite profiles in the American and Taiwanese populations, as well as some distinctive features. In both cases, two metabolites--4-cresyl sulfate (4CS) and phenylacetylglutamine (PAG)--were positively associated with age. In addition, creatine and β-hydroxy-β-methylbutyrate (HMB) were negatively correlated with age in both populations (p < 4 × 10⁻⁶). These age-associated gradients in creatine and HMB reflect decreasing muscle mass with age. The systematic increase in PAG and 4CS was confirmed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). Both are products of concerted microbial-mammalian host cometabolism and indicate an age-related association with the balance of host-microbiome metabolism.

Microbiota diversity and stability of the preterm neonatal ileum and colon of two infants

The composition of the microbiota associated with the human ileum and colon in the early weeks of life of two preterm infants was examined, with particular emphasis on the Lactobacillus and Bifidobacterium members. Culturing work showed that bifidobacteria and lactobacilli in the ileostomy changed over time, compared with the colostomy effluent where there was far less variation. The colostomy infant was dominated by two phyla, Actinobacteria and Firmicutes, while in the ileostomy samples, Proteobacteria emerged at the expense of Actinobacteria. Bacteroidetes were only detected following the reversal of the ileostomy in the final fecal sample and were not detected in any colonic fluid samples. Clostridia levels were unstable in the colostomy fluid, suggesting that the ileostomy/colostomy itself influenced the gut microbiota, in particular the strict anaerobes. Pyrosequencing analysis of microbiota composition indicated that bifidobacteria and lactobacilli are among the dominant genera in both the ileal and colonic fluids. Bifidobacteria and lactobacilli levels were unstable in the ileostomy fluid, with large reductions in numbers and relative proportions of both observed. These decreases were characterized by an increase in proportions of Streptococcus and Enterobacteriaceae. Clostridium was detected only in the colonic effluent, with large changes in the relative proportions over time.

Microbial composition of human appendices from patients following appendectomy

The human appendix has historically been considered a vestige of evolutionary development with an unknown function. While limited data are available on the microbial composition of the appendix, it has been postulated that this organ could serve as a microbial reservoir for repopulating the gastrointestinal tract in times of necessity. We aimed to explore the microbial composition of the human appendix, using high-throughput sequencing of the 16S rRNA gene V4 region. Seven patients, 5 to 25 years of age, presenting with symptoms of acute appendicitis were included in this study. Results showed considerable diversity and interindividual variability among the microbial composition of the appendix samples. In general, however, Firmicutes was the dominant phylum, with the majority of additional sequences being assigned at various levels to Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. Despite the large diversity in the microbiota found within the appendix, however, a few major families and genera were found to comprise the majority of the sequences present. Interestingly, also, certain taxa not generally associated with the human intestine, including the oral pathogens Gemella, Parvimonas, and Fusobacterium, were identified among the appendix samples. The prevalence of genera such as Fusobacterium could also be linked to the severity of inflammation of the organ. We conclude that the human appendix contains a robust and varied microbiota distinct from the microbiotas in other niches within the human microbiome. The microbial composition of the human appendix is subject to extreme variability and comprises a diversity of biota that may play an important, as-yet-unknown role in human health.

There are currently limited data available on the microbial composition of the human appendix. It has been suggested, however, that it may serve as a “safe house” for commensal bacteria that can reinoculate the gut at need. The present study is the first comprehensive view of the microbial composition of the appendix as determined by high-throughput sequencing. We have determined that the human appendix contains a wealth of microbes, including members of 15 phyla. Important information regarding the associated bacterial diversity of the appendix which will help determine the role, if any, the appendix microbiota has in human health is presented.

Prevalence and characterization of Clostridium perfringens from the faecal microbiota of elderly Irish subjects

The aim of this study was to investigate the diversity and composition of the intestinal microbiota of elderly subjects using a combination of culture-dependent techniques and 16S rRNA gene amplicon sequencing. The study was performed as part of the ELDERMET project, in which 368 faecal samples were assessed for viable numbers of Bifidobacterium spp., Lactobacillus spp. and Enterobacteriaceae on selective agar. However, the Bifidobacterium selective medium used also supported the growth of Clostridium perfringens, which appeared as distinct colonies and were subsequently characterized phenotypically and genotypically. All the isolates were confirmed as toxin biotype A producers. In addition, three isolates tested also had the genetic determinants for the β2 toxin. Of the 368 faecal samples assessed, C. perfringens was detected in 28 samples (7.6%). Moreover, C. perfringens was observed in samples from subjects in all the residence locations assessed but was most prevalent in subjects from long-stay residential care, with 71.4% of the samples (63.2% of the subjects) being from this residence location, and with a shedding level in excess of 10(6) c.f.u. (g faeces)(-1). Microbiota profiling revealed some significant compositional changes across both the family and genus taxonomic levels between the C. perfringens-positive and -negative datasets. Levels of culturable Bifidobacterium spp. and Lactobacillus spp. were significantly (P<0.05) lower in the C. perfringens-positive samples. Sequence-based methods also confirmed a significant difference in the Bifidobacterium spp. level (P<0.05) between both datasets. Taken together, these data suggest that a high viable count [>10(6) c.f.u. (g faeces)(-1)] of C. perfringens in stool samples may be indicative of a less healthy microbiota in the intestine of elderly people in long-stay residential care.

Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy

OBJECTIVES

The human intestinal microbiota composition alters naturally with age, but is unusually perturbed by antibiotic therapy. The impact of antibiotic therapy on the composition of the intestinal microbiota of a cross-section of elderly Irish subjects (n = 185, ≥ 65 years) was investigated, taking into consideration their residence location.

METHODS

Forty-two of the 185 elderly subjects were treated with at least one antibiotic within 1 month prior to faecal microbiota profiling. The residence locations of the subjects varied from long-term nursing care and rehabilitation wards to day hospitals and the community.

RESULTS

Culture-dependent methods indicated that faecal Bifidobacterium spp. numbers were significantly reduced following antibiotic treatment (P = 0.004, 7-fold reduction), while levels of Lactobacillus spp. and Enterobacteriaceae were unaffected. The largest decrease in Bifidobacterium spp. numbers was linked to the administration of nucleic acid synthesis inhibitors (P = 0.004, 23-fold reduction). Microbiota profiling revealed a significant compositional change across nine genera following antibiotic therapy, including a relative increase in Lactobacillus spp. (P = 0.031), as well as a decrease in the number of genera identified in the antibiotic-treated subjects (n = 58), when compared with untreated subjects (n = 79). More alterations in the intestinal microbiota were observed post-nucleic acid synthesis inhibitor therapy, most notably a decrease in relative Faecalibacterium spp. numbers (P < 0.001).

CONCLUSIONS

The impact of antibiotic therapy on the intestinal microbiota in the elderly should be considered for long-term health effects, and differential susceptibility may require the development of products (e.g. prebiotics and probiotics) for at-risk subjects.

High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin

The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

Clostridium difficile carriage in elderly subjects and associated changes in the intestinal microbiota

Clostridium difficile is an important nosocomial pathogen associated particularly with diarrheal disease in elderly individuals in hospitals and long-term care facilities. We examined the carriage rate of Clostridium difficile by culture as a function of fecal microbiota composition in elderly subjects recruited from the community, including outpatient, short-term respite, and long-term hospital stay subjects. The carriage rate ranged from 1.6% (n = 123) for subjects in the community, to 9.5% (n = 43) in outpatient settings, and increasing to 21% (n = 151) for patients in short- or long-term care in hospital. The dominant 072 ribotype was carried by 43% (12/28) of subjects, while the hypervirulent strain R027 (B1/NAP1/027) was isolated from 3 subjects (11%), 2 of whom displayed C. difficile associated diarrhea (CDAD) symptoms at the time of sampling. Emerging ribotypes with enhanced virulence (078 and 018) were also isolated from two asymptomatic subjects. Pyrosequencing of rRNA gene amplicons was used to determine the composition of the fecal microbiota as a surrogate for the microbial population structure of the distal intestine. Asymptomatic subjects (n = 20) from whom C. difficile was isolated showed no dramatic difference at the phylum or family taxonomic level compared to those that were culture negative (n = 252). However, in contrast, a marked reduction in microbial diversity at genus level was observed in patients who had been diagnosed with CDAD at the time of sampling and from whom C. difficile R027 was isolated.

Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice

OBJECTIVE

To investigate deep and comprehensive analysis of gut microbial communities and biological parameters after prebiotic administration in obese and diabetic mice.

RESEARCH DESIGN AND METHODS

Genetic (ob/ob) or diet-induced obese and diabetic mice were chronically fed with prebiotic-enriched diet or with a control diet. Extensive gut microbiota analyses, including quantitative PCR, pyrosequencing of the 16S rRNA, and phylogenetic microarrays, were performed in ob/ob mice. The impact of gut microbiota modulation on leptin sensitivity was investigated in diet-induced leptin-resistant mice. Metabolic parameters, gene expression, glucose homeostasis, and enteroendocrine-related L-cell function were documented in both models.

RESULTS

In ob/ob mice, prebiotic feeding decreased Firmicutes and increased Bacteroidetes phyla, but also changed 102 distinct taxa, 16 of which displayed a >10-fold change in abundance. In addition, prebiotics improved glucose tolerance, increased L-cell number and associated parameters (intestinal proglucagon mRNA expression and plasma glucagon-like peptide-1 levels), and reduced fat-mass development, oxidative stress, and low-grade inflammation. In high fat-fed mice, prebiotic treatment improved leptin sensitivity as well as metabolic parameters.

CONCLUSIONS

We conclude that specific gut microbiota modulation improves glucose homeostasis, leptin sensitivity, and target enteroendocrine cell activity in obese and diabetic mice. By profiling the gut microbiota, we identified a catalog of putative bacterial targets that may affect host metabolism in obesity and diabetes.