Biology subjects

Lavrinienko, A.

Publications and source records attributed to Lavrinienko, A..

2 recordsLinked to original sources

bioRxiv2025

Tier-based standards for FAIR sequence data and metadata sharing in microbiome research

Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (1) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (2) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and in three case studies of soil and gut microbiota used to manually validate the evaluation tool (n = 370), we found nearly half of publications do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes the (i) ineffectiveness of sequence data availability statements, and (ii) lack of consistent metadata reports used for annotation of microbial data. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate microbiome data reuse, supporting best practices that make microbiome data FAIR. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/636914v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@aaa4e8org.highwire.dtl.DTLVardef@130a3b1org.highwire.dtl.DTLVardef@4acc8aorg.highwire.dtl.DTLVardef@ba8688_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Covariation between metabolic and radioactive dose rates in Chornobyl rodents

High metabolic rate may provide fitness benefits for individuals. But high metabolic rates incur energetic costs and the need to ingest more food, increasing the risks of ingesting harmful substances from the environment. How organisms respond to elevated levels of ionizing radiation is an important question in the light of increasing pollution from nuclear accidents and waste, as well as ever-increasing reliance on radiation in medical diagnostics and therapies. We investigated how limits to metabolic rate, and aerobic metabolic scope (ceiling of energetic activity above maintenance levels), of wild rodents inhabiting a gradient of radioactive contamination from the Chernobyl accident covary with the biological burden of radionuclides in their bodies. Our results demonstrate that high biological dose rate correlates with high self-maintenance and low aerobic capacity in adults. In contrast, in subadults high dose rate correlates with high aerobic capacity. Consequently, high dose rate correlates with low aerobic scope in adults, but with high aerobic scope in subadults. Despite the uncertainty of the causal mechanisms, whether the dose rate affects the metabolic rate, the reverse or the reciprocal feedback prevail, it can be hypothesized that metabolic down-regulation could contribute to protection against radioactive exposure. Yet, metabolic down-regulation might be constrained by developmental obligations. Understanding the physiological mechanisms affecting responses to radiation exposure is key for risk assessment of environmental contamination, radiotherapies, and space exploration, and may help to rectify discordant opinions concerning the effects of radiation on the ecology of organisms living in Chornobyl.

ecology↗