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Evaluation of quality and biochemical properties of bovine meat from different rearing systems
Vukasinovic, Aleksandra; Fiorani, Federico; Costanzi, Egidia; Cataldi, Samuela; Pieroni, Luca; Cenci-Goga, Beniamino Terzo (Codon Publications, 2025-07)
The quality of meat plays an important role in maintaining human health. The aim of this study was to characterize the quality traits (color, marbling, and tenderness) of the Longissimus thoracis muscle and to compare the antioxidant capacity, phospholipid (PL) composition, and advanced glycation end products (AGEPs) in the diaphragm of beef from organic and traditional farming. Additionally, the effects of short supply chains (SSCs) and long supply chains (LSCs) were compared. For statistical analysis, t-tests and ANOVA were used. The results demonstrated that meat from organically raised animals had 1.7 times higher antioxidant power, richer in PL content by 1.25 and 1.12 times, and cholesterol levels were 3.38 and 2.84 times higher than meat from traditionally raised animals in both SSCs and LSCs, respectively. Conversely, the LSC doubled the value of AGEPs in organic meat.
Net rate of lateral gene transfer in marine prokaryoplankton
Stepanauskas, Ramunas; Brown, Julia M.; Arasti, Shayesteh; Mai, Uyen; Gavelis, Gregory; Pachiadaki, Maria; Bezuidt, Keoagile Ignatius Oliver; Munson-McGee, Jacob H.; Chang, Tianyi; Biller, Steven J.; Berube, Paul M.; Mirarab , Siavash (Oxford University Press, 2025-01)
Lateral gene transfer is a major evolutionary process in Bacteria and Archaea. Despite its importance, lateral gene transfer quantification in nature using traditional phylogenetic methods has been hampered by the rarity of most genes within the enormous microbial pangenomes. Here, we estimated lateral gene transfer rates within the epipelagic tropical and subtropical ocean using a global, randomized collection of single amplified genomes and a non-phylogenetic computational approach. By comparing the fraction of shared genes between pairs of genomes against a lateral gene transfer-free model, we show that an average cell line laterally acquires and retains ~13% of its genes every 1 million years. This translates to a net lateral gene transfer rate of ~250 genes L-1 seawater day-1 and involves both "flexible" and "core" genes. Our study indicates that whereas most genes are exchanged among closely related cells, the range of lateral gene transfer exceeds the contemporary definition of bacterial species, thus providing prokaryoplankton with extensive genetic resources for lateral gene transfer-based adaptation to environmental stressors. This offers an important starting point for the quantitative analysis of lateral gene transfer in natural settings and its incorporation into evolutionary and ecosystem studies and modeling.
Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives
Bustos-Caparros , Esteban; Viver , Tomeu; Gago, Juan F.; Avontuur, Juanita R.; Amiour, Souad; Baxter, Bonnie K .; Llames, María E.; Mutlu, Mehmet B.; Oren, Aharon; Ramírez, Ana S.; Stott, Matthew B.; Venter, S.N. (Stephanus Nicolaas); Santos , Fernando; Antón, Josefa; Rodriguez-R, Luis M.; Bosch, Rafael; Hedlund, Brian P.; Konstantinidis, Konstantinos T.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > Average Nucleotide Identity [ANI] > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.
Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it
Bustos-Caparros, Esteban; Viver, Tomeu; Gago, Juan F.; Venter, S.N. (Stephanus Nicolaas); Bosch, Rafael; Konstantinidis, Konstantinos T.; Rodriguez-R, Luis M.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.
Current status and future direction of antimicrobial stewardship programs and antibiotic prescribing in primary care hospitals in Zambia
Makiko, Faustina; Kalungia, Aubrey Chichonyi; Kampamba, Martin; Mudenda, Steward; Schellack, Natalie; Meyer, Johanna Catharina; Bumbangi, Flavien Nsoni; Okorie, Michael; Banda, David; Munkombwe, Derick; Mutwale, Ilunga; Chizimu, Joseph Yamweka; Kasanga, Maisa Anita; Masaninga, Freddie; Muhimba, Zoran; Lukwesa, Chileshe; Chanda, Duncan; Chanda, Raphael; Mpundu, Mirfin; Mwila, Chiluba; St. Claire-Jones, Anja; Newport, Melanie; Chilengi, Roma; Sefah, Israel Abebrese; Godman, Brian (Oxford University Press, 2025-06)
BACKGROUND : Antimicrobial Stewardship Programs (ASPs) intended to optimize antibiotic use will be more effective if informed by the current status and patterns of antibiotic utilisation. In Zambia's primary healthcare (PHC) settings, data on ASPs and antibiotic utilisation were inadequate to guide improvements. As a first step, this study assessed antibiotic prescribing and ASP core elements among PHC first-level hospitals (FLHs) in Zambia. METHODS : A point prevalence survey was conducted at the five FLHs in Lusaka using the Global-PPS® protocol. Hospital ASP core elements evaluated included hospital leadership commitment, accountability, pharmacy expertise, action, tracking, reporting, and education. RESULTS : Antibiotic use prevalence was 79.8% (146/183). A total of 220 antibiotic prescription encounters were recorded among inpatients, with ceftriaxone (J01DD04, Watch) being the most (50.0%) prescribed. Over 90.0% (202) of the antibiotic prescriptions targeted suspected community-acquired infections, but only 36.8% (81) were compliant with national treatment guidelines. ASP core element implementation was 36.0% (16.2/45), with only two hospitals achieving over 50.0%. The most deficient core elements were accountability, action, tracking, and reporting. CONCLUSIONS : ASP implementation in Zambia's FLHs providing PHC was sub-optimal, with high antibiotic prescribing rates, frequent use of broad-spectrum Watch group antibiotics, and low compliance with national treatment guidelines. As key ways forward, ASPs in Zambia's PHC require strengthening by adapting the WHO AWaRe recommendations and improving accountability, actions, tracking, and reporting antibiotic use to improve stewardship practice and reduce AMR.