Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx

The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria, and in the nostril, Firmicutes and Actinobacteria. In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups

The VLA-COSMOS 3 GHz Large Project: Average radio spectral energy distribution of active galactic nuclei

As the SKA is expected to be operational in the next decade, investigations of the radio sky in the range of 100 MHz to 10 GHz have become important for simulations of the SKA observations. In determining physical properties of galaxies from radio data, the radio SED is often assumed to be described by a simple power law, usually with a spectral index of 0.7 for all sources. Even though radio SEDs have been shown to exhibit deviations from this assumption, both in differing spectral indices and complex spectral shapes, it is often presumed that their individual differences cancel out in large samples. We constructed the average radio SED of radio-excess active galactic nuclei (RxAGN), defined as those that exhibit a 3 $\sigma$ radio luminosity excess with respect to the value expected only from contribution from star formation, out to z~4. We combined VLA observations of the COSMOS field at 1.4 GHz and 3 GHz with GMRT observations at 325 MHz and 610 MHz. To account for nondetections in the GMRT maps, we employed the survival analysis technique. We selected a sample of RxAGN out to z~4. We find that a sample of RxAGN can be described by a spectral index of $\alpha_1=0.28\pm0.03$ below the break frequency $\nu_b=(4.1\pm0.2)$ GHz and $\alpha_2=1.16\pm0.04$ above, while a simple power-law model yields a single spectral index of $\alpha=0.64\pm0.07$. By binning in 1.4 GHz radio luminosity and redshift, we find that the power-law spectral index, as well as broken power-law spectral indices, may increase for larger source sizes, while the power-law spectral index and lower-frequency (<4 GHz) broken power-law spectral index are additionally positively correlated with redshift.Comment: 12 pages, 11 figure

Genotypic diversity within a natural coastal bacterioplankton population

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science 307 (2005): 1311-1313, doi:10.1126/science.1106028.The genomic diversity and relative importance of unique genotypes within natural bacterial populations has remained largely unknown. Here, we analyze the diversity and annual dynamics of a group of coastal bacterioplankton (>99% 16S rRNA identity to Vibrio splendidus). We show that this group consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average <1 cell/ml). Overall, the genomes show extensive allelic diversity and size variation. Individual genotypes rarely recurred in samples and allelic distribution did not show spatial or temporal substructure. Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral.This work was supported by grants from the Department of Energy Genomes to Life program and the National Science Foundation. Sequences have been submitted to Genbank under accession numbers AY836800-AY837464

Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status

Background and objective: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. Design: Stimulated saliva samples from 292 participants with low levels of dental caries and periodontitis, enrolled in the Danish Health Examination Survey (DANHES), were analyzed for the presence of approximately 300 bacterial species by means of the Human Oral Microbe Identification Microarray (HOMIM). Using presence and levels (mean HOMIM-value) of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann–Whitney tests with Benjamini–Hochberg’s correction for multiple comparisons and principal component analysis. Results: Targets for 131 different probes were identified in 292 samples, with Streptococcus and Veillonella being the most predominant genera identified. Two bacterial taxa (Streptococcus sobrinus and Eubacterium [11][G-3] brachy) were more associated with smokers than non-smokers (adjusted p-value\u3c0.01). Stratification of the group based on extreme ends of the parameters age, gender, alcohol consumption, body mass index (BMI), and diet intake had no statistical influence on the composition of the bacterial profile of saliva. Conversely, differences in socioeconomic status were reflected by the bacterial profiles of saliva. Conclusions: The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status

Faraday tomography of LoTSS-DR2 data: I. Faraday moments in the high-latitude outer Galaxy and revealing Loop III in polarisation

Interstellar matter and star formatio

Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean

Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone. Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated. Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups

Microbial community succession on developing lesions on human enamel

Dental caries is one of the most common diseases in the world. However, our understanding of how the microbial community composition changes in vivo as caries develops is lacking.An in vivo model was used in a longitudinal cohort study to investigate shifts in the microbial community composition associated with the development of enamel caries.White spot lesions were generated in vivo on human teeth predetermined to be extracted for orthodontic reasons. The bacterial microbiota on sound enamel and on developing carious lesions were identified using the Human Oral Microbe Identification Microarray (HOMIM), which permits the detection of about 300 of the approximate 600 predominant bacterial species in the oral cavity.After only seven weeks, 75% of targeted teeth developed white spot lesions (8 individuals, 16 teeth). The microbial community composition of the plaque over white spot lesions differed significantly as compared to sound enamel. Twenty-five bacterial taxa, including Streptococcus mutans, Atopobium parvulum, Dialister invisus, and species of Prevotella and Scardovia, were significantly associated with initial enamel lesions. In contrast, 14 bacterial taxa, including species of Fusobacterium, Campylobacter, Kingella, and Capnocytophaga, were significantly associated with sound enamel.The bacterial community composition associated with the progression of enamel lesions is specific and much more complex than previously believed. This investigation represents one of the first longitudinally-derived studies for caries progression and supports microbial data from previous cross-sectional studies on the development of the disease. Thus, the in vivo experiments of generating lesions on teeth destined for extraction in conjunction with HOMIM analyses represent a valid model to study succession of supragingival microbial communities associated with caries development and to study efficacy of prophylactic and restorative treatments

A super-linear ‘radio-AGN main sequence’ links mean radio-AGN power and galaxy stellar mass since z ∼ 3

Mapping the average active galactic nucleus (AGN) luminosity across galaxy populations and over time reveals important clues regarding the interplay between supermassive black hole and galaxy growth. This paper presents the demography, mean power, and cosmic evolution of radio AGN across star-forming galaxies (SFGs) of different stellar masses (ℳ*). We exploit deep VLA-COSMOS 3 GHz data to build the rest-frame 1.4 GHz AGN luminosity functions at 0.1 ≤ z ≤ 4.5 hosted in SFGs. Splitting the AGN luminosity function into different ℳ* bins reveals that, at all redshifts, radio AGN are both more frequent and more luminous in higher ℳ* than in lower ℳ* galaxies. The cumulative kinetic luminosity density exerted by radio AGN in SFGs peaks at z ∼ 2, and it is mostly driven by galaxies with 10.5 ≤ log(ℳ*/ℳ⊙) < 11. Averaging the cumulative radio AGN activity across all SFGs at each (ℳ*,z) results in a ‘radio-AGN main sequence’ that links the time-averaged radio-AGN power ⟨L1.4AGN⟩ and galaxy stellar mass, in the form: log ⟨[L1.4AGN/ W Hz−1]⟩ = (20.97 ± 0.16) + (2.51 ± 0.34)⋅ log(1+z) + (1.41 ± 0.09)⋅(log[ℳ*/ℳ⊙] – 10). The super-linear dependence on ℳ*, at fixed redshift, suggests enhanced radio-AGN activity in more massive SFGs as compared to star formation. We ascribe this enhancement to both a higher radio AGN duty cycle and a brighter radio-AGN phase in more massive SFGs. A remarkably consistent ℳ* dependence is seen for the evolving X-ray AGN population in SFGs. This similarity is interpreted as possibly driven by secular cold gas accretion fuelling both radio and X-ray AGN activity in a similar fashion over the galaxy’s lifetime

A super-linear 'radio-AGN main sequence' links mean radio-AGN power and galaxy stellar mass since z similar to 3

Mapping the average active galactic nucleus (AGN) luminosity across galaxy populations and over time reveals important clues regarding the interplay between supermassive black hole and galaxy growth. This paper presents the demography, mean power, and cosmic evolution of radio AGN across star-forming galaxies (SFGs) of different stellar masses (M).We exploit deep VLA-COSMOS 3 GHz data to build the rest-frame 1.4 GHz AGN luminosity functions at 0:1 z 4:5 hosted in SFGs. Splitting the AGN luminosity function into different M bins reveals that, at all redshifts, radio AGN are both more frequent and more luminous in higher M than in lower M galaxies. The cumulative kinetic luminosity density exerted by radio AGN in SFGs peaks at z 2, and it is mostly driven by galaxies with 10:5 log(M=M ) < 11. Averaging the cumulative radio AGN activity across all SFGs at each (M,z) results in a ‘radio-AGN main sequence’ that links the time-averaged radio-AGN power hLAGN 1:4 i and galaxy stellar mass, in the form: log h[LAGN 1:4 /WHz1]i = (20.97 0.16) + (2.51 0.34) log(1+z) + (1.41 0.09) (log[M /M ] – 10). The super-linear dependence on M , at fixed redshift, suggests enhanced radio-AGN activity in more massive SFGs as compared to star formation. We ascribe this enhancement to both a higher radio AGN duty cycle and a brighter radio-AGN phase in more massive SFGs. A remarkably consistent M dependence is seen for the evolving X-ray AGN population in SFGs. This similarity is interpreted as possibly driven by secular cold gas accretion fuelling both radio and X-ray AGN activity in a similar fashion over the galaxy’s lifetime.The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation, the Villum Fonden, European Union’s Horizon research and innovation program under the Marie Skłodowska-Curie grant and the Italian Ministry of University and Research.http://www.hanspub.org/Journal/AAS.htmlam2023Physic

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination