Gaia Data Release 3 Creevey, O. L.; Sordo, R.; Pailler, F. ...
Astronomy and astrophysics (Berlin),
06/2023, Volume:
674
Journal Article
Peer reviewed
Open access
Gaia
Data Release 3 contains a wealth of new data products for the community. Astrophysical parameters are a major component of this release, and were produced by the Astrophysical parameters ...inference system (Apsis) within the
Gaia
Data Processing and Analysis Consortium (DPAC). The aim of this paper is to describe the overall content of the astrophysical parameters in
Gaia
DR3 and how they were produced. In Apsis, we use the mean BP/RP and mean RVS spectra along with astrometry and photometry, and we derive the following parameters: source classification and probabilities for 1.6 billion objects; interstellar medium characterisation and distances for up to 470 million sources, including a 2D total Galactic extinction map; 6 million redshifts of quasar candidates; 1.4 million redshifts of galaxy candidates; and an analysis of 50 million outlier sources through an unsupervised classification. The astrophysical parameters also include many stellar spectroscopic and evolutionary parameters for up to 470 million sources. These comprise
T
eff
, log
g
, and M/H (470 million using BP/RP, 6 million using RVS), radius (470 million), mass (140 million), age (120 million), chemical abundances (up to 5 million), diffuse interstellar band analysis (0.5 million), activity indices (2 million), H
α
equivalent widths (200 million), and further classification of spectral types (220 million) and emission-line stars (50 000). This paper is the first in a series of three papers, and focusses on describing the global content of the parameters in
Gaia
DR3. The accompanying Papers II and III focus on the validation and use of the stellar and non-stellar products, respectively. This catalogue is the most extensive homogeneous database of astrophysical parameters to date, and is based uniquely on
Gaia
data. It will only be superseded by
Gaia
Data Release 4, and will therefore remain a key reference over the next four years, providing astrophysical parameters independent of other ground- and space-based data.
Humans are host to a multitude of microorganisms that rapidly populate the body at birth, subject to a complex interplay that is dependent on host genetics, lifestyle, and environment. The ...host-associated microbiome, including the oral microbiome, presents itself in a complex ecosystem important to health and disease. As the most common chronic disease globally, dental caries is induced by host-microbial dysbiosis in children and adults. Multiple biological and environmental factors are likely to impact disease predisposition, onset, progression, and severity, yet longitudinal studies able to capture these influences are missing. To investigate how host genetics and environment influenced the oral microbial communities over time, we profiled supragingival plaque microbiomes of dizygotic and monozygotic twins during 3 visits over 12-months. Dental plaque DNA samples were amplified by targeting the 16S rRNA gene V4 region, and microbial findings were correlated with clinical, diet and genetic metadata. We observed that the oral microbiome variances were shaped primarily by the environment when compared to host genetics. Among the environmental factors shaping microbial changes of our subjects, significant metadata included age of the subject, and the age by which subjects initiated brushing habits, and the types of actions post-brushing. Relevant heritability of the microbiome included Actinomyces and Capnocytophaga in monozygotic twins and Kingella in dizygotic twins. Corynebacterium and Veillonella abundances were associated with age, whereas Aggregatibacter was associated with younger subjects. Streptococcus abundance showed an inverse association over time, and Selenomonas abundances increased with brushing frequency per day. Unraveling the exact biological mechanisms in caries has the potential to reveal novel host-microbial biomarkers, pathways, and targets important to effective preventive measures, and early disease control in children.
Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been ...postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.
Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant ...forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.
Long-duration spaceflight impacts human physiology, including well documented immune system dysregulation. The space food system has the potential to serve as a countermeasure to maladaptive ...physiological changes during spaceflight. However, the relationship between dietary requirements, the food system, and spaceflight adaptation requires further investigation to adequately define countermeasures and prioritize resources on future spaceflight missions. We evaluated the impact of an enhanced spaceflight diet, with increased quantity and variety of fruits, vegetables, fish, and other foods rich in flavonoids and omega-3 fatty acids, compared to a standard spaceflight diet on multiple health and performance outcomes in 16 subjects over four 45-day closed chamber missions in the NASA Human Exploration Research Analog (HERA). Subjects consuming the enhanced spaceflight diet had lower cholesterol levels, lower stress (i.e. cortisol levels), better cognitive speed, accuracy, and attention, and a more stable microbiome and metatranscriptome than subjects consuming the standard diet. Although no substantial changes were observed in the immune response, there were also no immune challenges, such as illness or infection, so the full benefits of the diet may not have been apparent in these analog missions. These results indicate that a spaceflight diet rich in fruits, vegetables, and omega-3 fatty acids produces significant health and performance benefits even over short durations. Further investigation is required to fully develop dietary countermeasures to physiological decrements observed during spaceflight. These results will have implications for food resource prioritization on spaceflight missions.
The skin is a complex living ecosystem harboring diverse microbial communities. Its highly variable properties and influence of intrinsic and extrinsic factors creates unique microenvironments where ...niche-specific microbes thrive. As part of the skin, hair supports its own microbial habitat that is also intra and inter-personal variable. This little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. To further investigate this, we explored the hair microbiota from scalp and pubic regions in healthy adults to investigate how the hair shaft microenvironment varies microbially. Our results suggest that there are distinct differences between the microbial communities identified on hair shafts originating from different parts of the body. The taxonomic composition of the communities from different hair sources are most reminiscent of those identified from their associated cutaneous region. We further demonstrate that the hair microbiota varies by geographical origin and has the potential to be used to predict the source location of the hair.
Gaia Data Release 3 Andrae, R.; Fouesneau, M.; Sordo, R. ...
Astronomy and astrophysics (Berlin),
06/2023, Volume:
674, Issue:
A27
Journal Article
Peer reviewed
Open access
Context.
The astrophysical characterisation of sources is among the major new data products in the third
Gaia
Data Release (DR3). In particular, there are stellar parameters for 471 million sources ...estimated from low-resolution BP/RP spectra.
Aims.
We present the General Stellar Parameterizer from Photometry (GSP-Phot), which is part of the astrophysical parameters inference system (Apsis). GSP-Phot is designed to produce a homogeneous catalogue of parameters for hundreds of millions of single non-variable stars based on their astrometry, photometry, and low-resolution BP/RP spectra. These parameters are effective temperature, surface gravity, metallicity, absolute
M
G
magnitude, radius, distance, and extinction for each star.
Methods.
GSP-Phot uses a Bayesian forward-modelling approach to simultaneously fit the BP/RP spectrum, parallax, and apparent
G
magnitude. A major design feature of GSP-Phot is the use of the apparent flux levels of BP/RP spectra to derive, in combination with isochrone models, tight observational constraints on radii and distances. We carefully validate the uncertainty estimates by exploiting repeat
Gaia
observations of the same source.
Results.
The data release includes GSP-Phot results for 471 million sources with
G
< 19. Typical differences to literature values are 110 K for
T
eff
and 0.2–0.25 for log
g
, but these depend strongly on data quality. In particular, GSP-Phot results are significantly better for stars with good parallax measurements (
ϖ
/
σ
ϖ
> 20), mostly within 2 kpc. Metallicity estimates exhibit substantial biases compared to literature values and are only useful at a qualitative level. However, we provide an empirical calibration of our metallicity estimates that largely removes these biases. Extinctions
A
0
and
A
BP
show typical differences from reference values of 0.07–0.09 mag. MCMC samples of the parameters are also available for 95% of the sources.
Conclusions.
GSP-Phot provides a homogeneous catalogue of stellar parameters, distances, and extinctions that can be used for various purposes, such as sample selections (OB stars, red giants, solar analogues etc.). In the context of asteroseismology or ground-based interferometry, where targets are usually bright and have good parallax measurements, GSP-Phot results should be particularly useful for combined analysis or target selection.
The leptin receptor-deficient db/db mouse model is an accepted in vivo model to study obesity, type 2 diabetes, and diabetic kidney disease. Healthy gastrointestinal (GI) microbiota has been linked ...to weight loss, improved glycemic control, and physiological benefits. We investigated the effect of various drugs on the GI microbiota of db/db mice as compared to control db/m mice. Treatment with long-acting pirfenidone (PFD) increased gut microbial diversity in diabetic db/db mice. Firmicutes, the most abundant phylum in db/m mice, decreased significantly in abundance in db/db mice but showed increased abundance with long-acting PFD treatment. Several bacterial taxa, including Lactobacillus and some Bacteroides, were less abundant in db/db mice and more abundant in long-acting-PFD-treated db/db mice. Long-acting PFD treatment reduced the abundance of Akkermansia muciniphila (5%) as compared to db/db mice (~15%). We conclude that gut microbial dysbiosis observed in db/db mice was partially reversed by long-acting PFD treatment and hypothesize that PFD has beneficial effects, in part, via its influence on the gut microbial metabolite profile. In quantitatively assessing urine metabolites, we observed a high abundance of diabetic ketoacidosis biomarkers, including 3-hydroxybutyric acid and acetoacetic acid in db/db mice, which were less abundant in the long-acting-PFD-treated db/db mice.
Gaia Data Release 3 Fouesneau, M.; Frémat, Y.; Andrae, R. ...
Astronomy and astrophysics (Berlin),
06/2023, Volume:
674
Journal Article
Peer reviewed
Open access
Context.
The third
Gaia
data release (
Gaia
DR3) contains, beyond the astrometry and photometry, dispersed light for hundreds of millions of sources from the
Gaia
prism spectra (BP and RP) and the ...spectrograph (RVS). This data release opens a new window on the chemo-dynamical properties of stars in our Galaxy, essential knowledge for understanding the structure, formation, and evolution of the Milky Way.
Aims.
To provide insight into the physical properties of Milky Way stars, we used these data to produce a uniformly derived all-sky catalogue of stellar astrophysical parameters: atmospheric properties (
T
eff
, log
g
, M/H,
α
/Fe, activity index, emission lines, and rotation), 13 chemical abundance estimates, evolution characteristics (radius, age, mass, and bolometric luminosity), distance, and dust extinction.
Methods.
We developed the astrophysical parameter inference system (Apsis) pipeline to infer astrophysical parameters of
Gaia
objects by analysing their astrometry, photometry, BP/RP, and RVS spectra. We validate our results against those from other works in the literature, including benchmark stars, interferometry, and asteroseismology. Here we assess the stellar analysis performance from Apsis statistically.
Results.
We describe the quantities we obtained, including the underlying assumptions and the limitations of our results. We provide guidance and identify regimes in which our parameters should and should not be used.
Conclusions.
Despite some limitations, this is the most extensive catalogue of uniformly inferred stellar parameters to date. They comprise
T
eff
, log
g
, and M/H (470 million using BP/RP, 6 million using RVS), radius (470 million), mass (140 million), age (120 million), chemical abundances (5 million), diffuse interstellar band analysis (half a million), activity indices (2 million), H
α
equivalent widths (200 million), and further classifications of spectral types (220 million) and emission-line stars (50 thousand). More precise and detailed astrophysical parameters based on epoch BP, RP, and RVS spectrophotometry are planned for the next
Gaia
data release.
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