The Gut Microbiota Composition in Dichorionic Triplet Sets Suggests a Role for Host Genetic Factors

peer-reviewedMonozygotic and dizygotic twin studies investigating the relative roles of host genetics and environmental factors in shaping gut microbiota composition have produced conflicting results. In this study, we investigated the gut microbiota composition of a healthy dichorionic triplet set. The dichorionic triplet set contained a pair of monozygotic twins and a fraternal sibling, with similar pre- and post-natal environmental conditions including feeding regime. V4 16S rRNA and rpoB amplicon pyrosequencing was employed to investigate microbiota composition, and the species and strain diversity of the culturable bifidobacterial population was also examined. At month 1, the monozygotic pair shared a similar microbiota distinct to the fraternal sibling. By month 12 however, the profile was more uniform between the three infants. Principal coordinate analysis (PCoA) of the microbiota composition revealed strong clustering of the monozygotic pair at month 1 and a separation of the fraternal infant. At months 2 and 3 the phylogenetic distance between the monozygotic pair and the fraternal sibling has greatly reduced and by month 12 the monozygotic pair no longer clustered separately from the fraternal infant. Pulse field gel electrophoresis (PFGE) analysis of the bifidobacterial population revealed a lack of strain diversity, with identical strains identified in all three infants at month 1 and 12. The microbiota of two antibiotic-treated dichorionic triplet sets was also investigated. Not surprisingly, in both triplet sets early life antibiotic administration appeared to be a major determinant of microbiota composition at month 1, irrespective of zygosity. By month 12, early antibiotic administration appeared to no longer exert such a strong influence on gut microbiota composition. We hypothesize that initially host genetics play a significant role in the composition of an individual’s gut microbiota, unless an antibiotic intervention is given, but by month 12 environmental factors are the major determinant.This study was performed as part of the INFANTMET project (10/RD/Infantmet/MFRC/705) and was funded by the Government of Ireland's Department of Agriculture Fisheries and in part by Alimentary Pharmabiotic Centre. KM is a Teagasc Walsh Fellow. CS, RPR and PWOT are members of The Alimentary Pharmabiotic Centre, which is a Centre for Science and Technology (CSET) funded by the Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan (Grant no. 02/CE/B124 and 07/CE/B1368)

The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

peer-reviewedHuman milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine

PANIC: A Near-infrared Camera for the Magellan Telescopes

PANIC (Persson's Auxiliary Nasmyth Infrared Camera) is a near-infrared camera designed to operate at any one of the f/11 folded ports of the 6.5m Magellan telescopes at Las Campanas Observatory, Chile. The instrument is built around a simple, all-refractive design that reimages the Magellan focal plane to a plate scale of 0.125'' pixel^{-1} onto a Rockwell 1024x1024 HgCdTe detector. The design goals for PANIC included excellent image quality to sample the superb seeing measured with the Magellan telescopes, high throughput, a relatively short construction time, and low cost. PANIC has now been in regular operation for over one year and has proved to be highly reliable and produce excellent images. The best recorded image quality has been ~0.2'' FWHM.Comment: 8 pages, 5 figures. To appear in "Astronomical Telescopes and Instrumentation," Proc SPIE (Glasgow), June 2004. Version with higher resolution figures is available at http://cfa-www.harvard.edu/~pmartini/professional/publications/panic.pd

Longitudinal Data Clustering with a Copula Kernel Mixture Model

Many common clustering methods cannot be used for clustering multivariate longitudinal data in cases where variables exhibit high autocorrelations. In this article, a copula kernel mixture model (CKMM) is proposed for clustering data of this type. The CKMM is a finite mixture model which decomposes each mixture component's joint density function into its copula and marginal distribution functions. In this decomposition, the Gaussian copula is used due to its mathematical tractability and Gaussian kernel functions are used to estimate the marginal distributions. A generalized expectation-maximization algorithm is used to estimate the model parameters. The performance of the proposed model is assessed in a simulation study and on two real datasets. The proposed model is shown to have effective performance in comparison to standard methods, such as K-means with dynamic time warping clustering and latent growth models

Observation of playa salts as nuclei in orographic wave clouds

During the Ice in Clouds Experiment-Layer Clouds (ICE-L), dry lakebed, or playa, salts from the Great Basin region of the United States were observed as cloud nuclei in orographic wave clouds over Wyoming. Using a counterflow virtual impactor in series with a single-particle mass spectrometer, sodium-potassium-magnesium-calcium-chloride salts were identified as residues of cloud droplets. Importantly, these salts produced similar mass spectral signatures to playa salts with elevated cloud condensation nuclei (CCN) efficiencies close to sea salt. Using a suite of chemical characterization instrumentation, the playa salts were observed to be internally mixed with oxidized organics, presumably produced by cloud processing, as well as carbonate. These salt particles were enriched as residues of large droplets (>19 μm) compared to smaller droplets (>7 μm). In addition, a small fraction of silicate-containing playa salts were hypothesized to be important in the observed heterogeneous ice nucleation processes. While the high CCN activity of sea salt has been demonstrated to play an important role in cloud formation in marine environments, this study provides direct evidence of the importance of playa salts in cloud formation in continental North America has not been shown previously. Studies are needed to model and quantify the impact of playas on climate globally, particularly because of the abundance of playas and expected increases in the frequency and intensity of dust storms in the future due to climate and land use changes

The Role of TLR2 and Bacterial Lipoprotein in Enhancing Airway Inflammation and Immunity

Non-typeable Haemophilus influenzae (NTHI) colonizes the lower respiratory tract of patients with chronic obstructive pulmonary disease and also causes exacerbations of the disease. The 16-kDa lipoprotein P6 has been widely studied as a potential vaccine antigen due to its highly conserved expression amongst NTHI strains. Although P6 is known to induce potent inflammatory responses, its role in the pathogenesis of NTHI infection in vivo has not been examined. Additionally, the presence of an amino-terminal lipid motif on P6 serves to activate host Toll-like receptor 2 (TLR2) signaling. The role of host TLR2 and NTHI expression of the lipoprotein P6 on the induction of airway inflammation and generation of adaptive immune responses following chronic NTHI stimulation was evaluated with TLR2-deficient mice and a P6-deficient NTHI strain. Absence of either host TLR2 or bacterial P6 resulted in diminished levels of immune cell infiltration within lungs of mice exposed to NTHI. Pro-inflammatory cytokine secretion was also reduced in lungs that did not express TLR2 or were exposed to NTHI devoid of P6. Induction of specific antibodies to P6 was severely limited in TLR2-deficient mice. Although mice exposed to the P6-deficient NTHI strain were capable of generating antibodies to other surface antigens of NTHI, these levels were lower compared to those observed in mice exposed to P6-expressing NTHI. Therefore, cognate interaction between host TLR2 and bacterial P6 serves to enhance lung inflammation and elicit robust adaptive immune responses during NTHI exposure. Strategies to limit NTHI inflammation while simultaneously promoting robust immune responses may benefit from targeting the TLR2:P6 signaling axis

Efficient Activation of Reconstructed Rat Embryos by Cyclin-Dependent Kinase Inhibitors

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Relationships of Biomass-Burning Aerosols to Ice in Orographic Wave Clouds

Ice concentrations in orographic wave clouds at temperatures between −24° and −29°C were shown to be related to aerosol characteristics in nearby clear air during five research flights over the Rocky Mountains. When clouds with influence from colder temperatures were excluded from the dataset, mean ice nuclei and cloud ice number concentrations were very low, on the order of 1–5 L^(−1). In this environment, ice number concentrations were found to be significantly correlated with the number concentration of larger particles, those larger than both 0.1- and 0.5-μm diameter. A variety of complementary techniques was used to measure aerosol size distributions and chemical composition. Strong correlations were also observed between ice concentrations and the number concentrations of soot and biomass-burning aerosols. Ice nuclei concentrations directly measured in biomass-burning plumes were the highest detected during the project. Taken together, this evidence indicates a potential role for biomass-burning aerosols in ice formation, particularly in regions with relatively low concentrations of other ice nucleating aerosols