Strain-resolved metagenomics approaches applied to biogas upgrading

Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count—two for both hydrogenotrophic archaea—and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

Background: The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. Results: The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. Conclusions: This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization

Die Bedeutung von Rhamnolipiden in der Pathogenese epithelialer Pseudomonas aeruginosa Infektionen

Pseudomonas aeruginosa (P. aeruginosa) ist ein ubiquitär vorkommendes, gramnegatives, monotrich begeißeltes, aerob lebendes Stäbchenbakterium. Das opportunistisches Pathogen befällt Menschen, Tiere, Insekten, Nematoden und Pflanzen und ist unter anderem aufgrund seiner Toleranz gegenüber einer Vielzahl von Desinfektionsmitteln und Antibiotika einer der wichtigsten Verursacher von nosokomialen Infektionen. Die Ergebnisse dieser Arbeit geben einen Hinweis darauf, dass P. aeruginosa das angeborene Immunsystem mit Hilfe von Rhamnolipid, einem vom Bakterium selbst produzierten Surfactant, umgeht. In der vorliegenden Arbeit konnte nachgewiesen werden, dass die Flagellin-induzierte hBD2-Expression in humanen Keratinozyten durch bakterielle Überstände von P. aeruginosa, die in der stationären Phase generiert wurden, supprimiert wird. Der supprimierende Faktor konnte in Versuchen als hitzestabil und durch Säure ausfällbar identifiziert werden. Außerdem blieb er bei Behandlung mit Proteinase K unbeeinflusst, es handelt sich deshalb nicht um ein Protein. Weitere Untersuchungen konnten den Faktor als Rhamnolipid identifizieren. Eine Kostimulation von Keratinozyten mit aufgereinigtem Rhamnolipid in Mengen unterhalb der zytotoxischen Konzentration zusammen mit Flagellin zeigte ebenfalls eine Supprimierung der induzierten hBD2-Expression. Ähnliche Effekte konnten bei Kostimulation der Keratinozyten mit Flagellin und BAPTA-AM, einem intrazellulären Calciumchelator, erreicht werden. Neben Flagellin als Induktor ließ sich auch die PMA-induzierte hBD2-Expression supprimieren. Dies lässt vermuten, dass Rhamnolipide mit Calcium-abhängigen Signalkaskaden, wie der PKC-Signalkaskade, interferieren. Die Versuche dieser Arbeit zeigen damit einen Weg, über den es P. aeruginosa möglich ist, sich auf der Haut zu etablieren, ohne seinen Hauptpathogenitätsfaktor, das Flagellin, verstecken zu müssen

Type 1 diabetes, diabetic nephropathy, and pregnancy: a systematic review and meta-study

BACKGROUND: In the last decade, significant improvements have been achieved in maternal-fetal and diabetic care which make pregnancy possible in an increasing number of type 1 diabetic women with end-organ damage. Optimal counseling is important to make the advancements available to the relevant patients and to ensure the safety of mother and child. A systematic review will help to provide a survey of the available methods and to promote optimal counseling. OBJECTIVES: To review the literature on diabetic nephropathy and pregnancy in type 1 diabetes. METHODS: Medline, Embase, and the Cochrane Library were scanned in November 2012 (MESH, Emtree, and free terms on pregnancy and diabetic nephropathy). Studies were selected that report on pregnancy outcomes in type 1 diabetic patients with diabetic nephropathy in 1980-2012 (i.e. since the detection of microalbuminuria). Case reports with less than 5 cases and reports on kidney grafts were excluded. Paper selection and data extraction were performed in duplicate and matched for consistency. As the relevant reports were highly heterogeneous, we decided to perform a narrative review, with discussions oriented towards the period of publication. RESULTS: Of the 1058 references considered, 34 fulfilled the selection criteria, and one was added from reference lists. The number of cases considered in the reports, which generally involved single-center studies, ranged from 5 to 311. The following issues were significant: (i) the evidence is scattered over many reports of differing format and involving small series (only 2 included over 100 patients), (ii) definitions are non-homogeneous, (iii) risks for pregnancy-related adverse events are increased (preterm delivery, caesarean section, perinatal death, and stillbirth) and do not substantially change over time, except for stillbirth (from over 10% to about 5%), (iv) the increase in risks with nephropathy progression needs confirmation in large homogeneous series, (v) the newly reported increase in malformations in diabetic nephropathy underlines the need for further studies. CONCLUSIONS: The heterogeneous evidence from studies on diabetic nephropathy in pregnancy emphasizes the need for further perspective studies on this issue

Evidence for proton acceleration up to TeV energies based on VERITAS and Fermi-LAT observations of the Cas A SNR

We present a study of $\gamma$-ray emission from the core-collapse supernova remnant Cas~A in the energy range from 0.1GeV to 10TeV. We used 65 hours of VERITAS data to cover 200 GeV - 10 TeV, and 10.8 years of \textit{Fermi}-LAT data to cover 0.1-500 GeV. The spectral analysis of \textit{Fermi}-LAT data shows a significant spectral curvature around $1.3 \pm 0.4_{stat}$ GeV that is consistent with the expected spectrum from pion decay. Above this energy, the joint spectrum from \textit{Fermi}-LAT and VERITAS deviates significantly from a simple power-law, and is best described by a power-law with spectral index of $2.17\pm 0.02_{stat}$ with a cut-off energy of $2.3 \pm 0.5_{stat}$ TeV. These results, along with radio, X-ray and $\gamma$-ray data, are interpreted in the context of leptonic and hadronic models. Assuming a one-zone model, we exclude a purely leptonic scenario and conclude that proton acceleration up to at least 6 TeV is required to explain the observed $\gamma$-ray spectrum. From modeling of the entire multi-wavelength spectrum, a minimum magnetic field inside the remnant of $B_{\mathrm{min}}\approx150\,\mathrm{\mu G}$ is deduced.Comment: 33 pages, 9 Figures, 6 Table