Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations > 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.     

Early Life Origins of All-Cause and Cause-Specific Disability Pension: Findings from the Helsinki Birth Cohort Study

Background

There is some evidence linking sub-optimal prenatal development to an increased risk of disability pension (DP). Our aim was to investigate whether body size at birth was associated with transitioning into all-cause and cause-specific DP during the adult work career.

Methods

10 682 people born in 1934–44 belonging to the Helsinki Birth Cohort Study had data on birth weight extracted from birth records, and on time, type and reason of retirement between 1971 and 2011 extracted from the Finnish Centre for Pensions.

Results

Altogether 21.3% transitioned into DP during the 40-year follow-up, mainly due to mental disorders, musculoskeletal disorders and cardiovascular disease. Average age of transitioning into DP was 51.3 (SD 8.4) for men and 52.2 (SD 7.6) for women. Cohort members who did not transition into DP retired 10 years later on average. Among men, higher birth weight was associated with a lower hazard of transitioning into DP, adjusted hazard ratio (HR) being 0.94 (95% confidence interval [CI] 0.88–0.99 for 1 SD increase in birth weight). For DP due to mental disorders the adjusted HR was 0.90, 95% CI 0.81, 0.99. A similar but non-significant trend was found for DP due to cardiovascular disease. Among women there were no associations between body size at birth and all-cause DP (p for interaction gender*birth weight on DP p = 0.007).

Conclusions

Among men disability pension, particularly due to mental disorders, may have its origins in prenatal development. Given that those who retire due to mental health problems are relatively young, the loss to the workforce is substantial.     

Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms

Background

While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT)Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point.

Principal Findings

A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected.

Conclusions/Significance

A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the individual and common core microbiota in healthy adults. The findings provide new approaches to define intestinal health and to further characterize the microbial communities inhabiting the human gut.     

<Emphasis Type="Italic">Limnocnida tanganyicae</Emphasis> medusae (Cnidaria: Hydrozoa): a semiautonomous microcosm in the food web of Lake Tanganyika

Medusae are important members of marine food webs, but are rare in lakes. In one of the largest lakes in the world, Lake Tanganyika, a small medusa (Limnocnida tanganyicae) is a prominent component of zooplankton. We used field and laboratory methods to study the ecological role of Lake Tanganyika medusae, which occasionally reached high local densities in the whole epilimnion. The largest individuals showed low amplitude, diel vertical migration which minimized their exposure to harmful UV radiation and also may be important for picocyanobacteria regularly present in the medusae. The endosymbiotic picocyanobacteria differed morphologically among medusae and were predominantly one Lake Biwa type Cyanobium sp. that typically was abundant in the water column. Under light, some medusae were net primary producers. Although nitrogen stable isotopic ratios indicated that the free-living cyanobacteria were nitrogen-fixers, the picocyanobacteria in medusae obtained nitrogen predominantly from their host. Stable isotopic ratios of carbon and nitrogen further suggested that copepods were the most likely prey for the medusae. Lake Tanganyika medusae apparently base their metabolism both on animal and plant sources, with possible internal cycling of nutrients; however, the role of picocyanobacteria gardening in the Lake Tanganyika ecosystem and its medusae requires quantification.     

Lactobacillus rhamnosus GG Intake Modifies Preschool Children’s Intestinal Microbiota,Alleviates Penicillin-Associated Changes,and Reduces Antibiotic Use

Antibiotic use is considered among the most severe causes of disturbance to children’s developing intestinal microbiota, and frequently causes adverse gastrointestinal effects ranging from mild and transient diarrhoea to life-threatening infections. Probiotics are commonly advocated to help in preventing antibiotic-associated gastrointestinal symptoms. However, it is currently unknown whether probiotics alleviate the antibiotic-associated changes in children’s microbiota. Furthermore, it is not known how long-term probiotic consumption influences the developing microbiota of children. We analysed the influence of long-term Lactobacillus rhamnosus GG intake on preschool children’s antibiotic use, and antibiotic-associated gastrointestinal complaints in a double blind, randomized placebo-controlled trial with 231 children aged 2–7. In addition, we analysed the effect of L. rhanmosus GG on the intestinal microbiota in a subset of 88 children. The results show that long-term L. rhamnosus GG supplementation has an influence on the composition of the intestinal microbiota in children, causing an increase in the abundance of Prevotella, Lactococcus, and Ruminococcus, and a decrease in Escherichia. The treatment appeared to prevent some of the changes in the microbiota associated with penicillin use, but not those associated with macrolide use. The treatment, however, did reduce the frequency of gastrointestinal complaints after a macrolide course. Finally, the treatment appeared to prevent certain bacterial infections for up to 3 years after the trial, as indicated by reduced antibiotic use.Trial Registration: ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01014676","term_id":"NCT01014676"}}NCT01014676     

On-line biomass measurements in bioreactor cultivations: comparison study of two on-line probes

Two on-line probes for biomass measurement in bioreactor cultivations were evaluated. One probe is based on near infrared (NIR) light absorption and the other on dielectric spectroscopy. The probes were used to monitor biomass production in cultivations of several different microorganisms. Differences in NIR probe response compared to off-line measurement methods revealed that the most significant factor affecting the response was cell shape. The NIR light absorption method is more developed and reliable for on-line in situ biomass estimation than dielectric spectroscopy. The NIR light absorption method is, however, of no significant use, when the cultivation medium is not clear, and especially in processes using adsorbents or solid matrix for the microorganism to grow on. The possibilities offered by dielectric spectroscopy are impressive, but the on-line probe technology needs to be improved.