grenedalf: Population genetic statistics for the next generation of Pool sequencing

Bioinformatics, Год журнала: 2024, Номер 40(8)

Опубликована: Авг. 1, 2024

Abstract Summary Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written C++ that implements common population statistics θ, Tajima’s D, FST sequencing. It orders magnitude faster than current tools, focused on providing usability scalability, while also offering plethora input file formats convenience options. Availability implementation grenedalf published under the GPL-3, freely available at github.com/lczech/grenedalf.

Язык: Английский

---

The evaluation of biogenic silica in brackish and freshwater strains reveals links between phylogeny and silica accumulation in picocyanobacteria

Applied and Environmental Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Март 27, 2025

ABSTRACT Through biosilicification, organisms incorporate dissolved silica (dSi) and deposit it as biogenic (bSi), driving the silicon (Si) cycle in aquatic systems. While Si accumulation marine picocyanobacteria has been recently observed, its mechanisms ecological implications remain unclear. This study investigates biosilicification brackish of Synechococcus clade two model freshwater coccoid cyanobacteria. Brackish strains showed significantly higher quotas when supplemented with external dSi (100 µM) compared to controls (up 60.0 ± 7.3 amol Si.cell-1 versus 9.2 16.3 2.9 Si.cell-1). Conversely, displayed no significant differences between dSi-enriched treatments controls, emphasizing that not all phytoplanktons without an obligate requirement accumulate this element. The Si-accumulating clustered within clade, whereas their counterparts formed a distinct sister group, suggesting link phylogeny silicification. Rapid culture growth caused increased pH led precipitation, influencing apparent uptake; was mitigated by control through bubbling. phenomenon for natural systems affected phytoplankton blooms. In such environments, pH-induced precipitation may reduce availability impacting Si-dependent populations like diatoms. Our findings suggest could influence at least mechanisms: cellular biologically induced changes concentrations. IMPORTANCE work provides first evidence uncovers patterns. demonstrate picocyanobacterial induces pH-dependent which lead overestimations up 85%. process drive substantial highly productive coastal systems, potential effects on cycling population dynamics phytoplankton. extent modern offers insights into rock record, shedding light evolutionary sedimentary processes preservation signatures geological formations. Overall, research adds impact microorganisms lacking have dynamics.

Язык: Английский

---

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine

Gut Microbes, Год журнала: 2025, Номер 17(1)

Опубликована: Янв. 12, 2025

The therapeutic benefits of opioids are compromised by the development analgesic tolerance, which necessitates higher dosing for pain management thereby increasing liability drug dependence and addiction. Rodent models indicate opposing roles gut microbiota in tolerance: morphine-induced dysbiosis exacerbates whereas probiotics ameliorate tolerance. Not all individuals develop could be influenced differences microbiota, yet no study design has capitalized upon this natural variation. We leveraged behavioral variation a murine model voluntary oral morphine self-administration to elucidate mechanisms influences Although mice shared similar morphine-driven changes that largely masked informative associations with variability our high-resolution temporal analyses revealed divergence progression best explained sustained antinociception. Mice did not tolerance maintained capacity production short-chain fatty acid (SCFA) butyrate known bolster intestinal barriers promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor dietary supplementation significantly reduced independently suppression systemic inflammation. These findings inform immediate therapies extend efficacy opioids.

Язык: Английский

---

Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide

The Science of The Total Environment, Год журнала: 2020, Номер 751, С. 141799 - 141799

Опубликована: Авг. 19, 2020

Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well whole ecosystems. However, such remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning host health. We analysed bacterial communities sequencing 16S rRNA gene fragment amplicons following spray of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized Proteobacteria, Alphaproteobacteria accounting up to 33.8% indigenous community. Bioinformatic analyses indicated pesticide applications had an effect core microbiome rare microbiome. Moreover, interference found selective. have identified four positive responders including ASV assigned genus Acinetobacter 12 negative genera known beneficial plant-microbe interactions, Stenotrophomonas, Sphingomonas, Flavobacterium Serratia. Complementary inference community level microbes distinct stress response systems were likely enriched conducted treatments. overall findings confirmed treatments induce measureable shifts colonizing plant phyllosphere. They also indicate potentially bacteria, their intrinsic association plants, among most sensitive employed thus highlight importance off-target studies context

Язык: Английский

---

Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract

Scientific Reports, Год журнала: 2020, Номер 10(1)

Опубликована: Сен. 16, 2020

Abstract The gut microbiome is known to be sensitive changes in the immune system, especially during autoimmune diseases such as Multiple Sclerosis (MS). Our study examines that occur experimental encephalomyelitis (EAE), an animal model for MS. We collected fecal samples at key stages of EAE progression and quantified microbial abundances with 16S V3–V4 amplicon sequencing. analysis data suggests abundance commensal Lactobacillaceae decreases while other populations belonging Clostridiaceae, Ruminococcaceae, Peptostreptococcaceae families expand. Community co-occurrence networks points these three expanding taxa potential mediators dysbiosis. also employed PICRUSt2 impute MetaCyc Enzyme Consortium (EC) pathway from original data. From this analysis, we found a number imputed EC pathways responsible production immunomodulatory compounds appear enriched mice undergoing EAE. interpretation results provides detailed picture are occurring throughout course disease helps evaluate viable dysbiosis MS patients.

Язык: Английский

---