Altitude-dependent metabolite biomarkers reveal the mechanism of plateau pika adaptation to high altitudes

Animal Models of Human Disease 2.0

The use of animal models is crucial for advancing translational research by identifying effective treatment targets and strategies for clinical application in human disease [...].

Association between gut microbiota and male infertility: a two-sample Mendelian randomization study

Previous research has confirmed the significant association between gut microbiota (GM) and male infertility (MI), but the causality between them remains unclear. This study aims to investigate the causal relationship between GM and MI using Mendelian randomization (MR) and provide supplementary information for the optimization of future randomized controlled trials (RCTs). Instrumental variables for 211 GM taxa were obtained from genome-wide association studies (GWAS), and inverse variance weighted (IVW) method was used as the main analysis method for two-sample MR analysis to assess the impact of GM on the risk of MI. Four methods were used to test for horizontal pleiotropy and heterogeneity of MR results to ensure the reliability of the MR findings. A total of 50 single-nucleotide polymorphisms (SNPs) closely related to GM were included, and ultimately identified 1 family and 4 general are causally associated with MI. Among them, Anaerotruncus (OR = 1.96, 95% CI 1.31-3.40, P = 0.016) is significantly associated with increased MI risk. Furthermore, we used four MR methods to evaluate the causality, and the results supported these findings. The leave-one-out analysis showed stable results with no instrumental variables exerting strong influence on the results. The causal direction indicated a positive effect, and the effects of heterogeneity and horizontal pleiotropy on the estimation of causal effect were minimized. We confirmed a causal relationship between GM taxa and MI, providing new insights into the mechanisms underlying GM-mediated MI.

The mRNA N6-Methyladenosine Response to Dehydration in Xenopus laevis

The African clawed frog, Xenopus laevis, exhibits remarkable adaptations to survive in its arid habitat, including behavioral and metabolic changes during periods of drought. During extreme dehydration, X. laevis undergoes estivation, a state characterized by increased urea and ammonia levels, depression of the metabolic rate, and tissue hypoxia. To understand the molecular mechanisms underlying these adaptations, we investigated the potential role of N6-methyladenosine (m6A), a widespread mRNA modification, in X. laevis during extreme dehydration. We analyzed the protein levels of key components in the m6A pathway, including writers (METTL3, METTL14, and WTAP), erasers (ALKBH5 and FTO), and readers (SRSF3, YTHDF1, YTHDF2, YTHDF3, and eIF3a), in the liver and kidneys of control frogs and frogs that had lost 35 ± 0.93% of their total body water. The relative protein levels generally decreased or remained unchanged, with the exception of YTHDF3, which depicted a protein level increase in the liver. Notable changes included eIF3a, which was downregulated by 26 ± 8% and 80 ± 8% in the dehydrated liver and kidney tissues, respectively. Additionally, the total m6A increased by 353 ± 30% and 177 ± 17% in dehydrated liver and kidney RNA samples, respectively. This study highlights the importance of epigenetic mechanisms in stress tolerance and provides a foundation for further exploration of the role of epigenetics in dehydration tolerance.

Multi-omics analysis reveals the genetic and environmental factors in shaping the gut resistome of a keystone rodent species

Understanding the emergence and spread of antibiotic resistance genes (ARGs) in wildlife is critical for the health of humans and animals from a "One Health" perspective. The gut microbiota serve as a reservoir for ARGs; however, it remains poorly understood how environmental and host genetic factors influence ARGs by affecting the gut microbiota. To elucidate this, we analyzed whole-genome resequencing data from 79 individuals of Brandt's vole in two geographic locations with different antibiotics usage, together with metabolomic data and shotgun sequencing data. A high diversity of ARGs (851 subtypes) was observed in vole's gut, with a large variation in ARG composition between individuals from Xilingol and Hulunbuir in China. The diversity and composition of ARGs were strongly correlated with variations in gut microbiota community structure. Genome-wide association studies revealed that 803 loci were significantly associated (P<5.05×10-9) with 31 bacterial species, and bipartite networks identified 906 bacterial species-ARGs associations. Structural equation modeling analysis showed that host genetic factors, air temperature, and presence of pollutants (Bisphenol A) significantly affected gut microbiota community structure, which eventually regulated the diversity of ARGs. The present study advances our understanding of the complex host-environment interactions that underlie the spread of ARGs in the natural environments.

Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.

Impacts of climate change and human activities on three Glires pests of the Qinghai-Tibet Plateau

BACKGROUND

The range of Glires is influenced by human activities and climate change. However, the extent to which human activities and environmental changes have contributed to this relationship remains unclear. We examined alterations in the distribution changes and driving factors of the Himalayan marmot, plateau pika, and plateau zokor on the Qinghai-Tibet Plateau (QTP) using the maximum entropy (MaxEnt) model and a geographical detector (Geodetector).

RESULTS

The MaxEnt model showed that the contribution rates of the human footprint index (HFI) to the distribution patterns of the three types of Glires were 46.70%, 58.70%, and 59.50%, respectively. The Geodetector results showed that the distribution pattern of the Himalayan marmot on the QTP was influenced by altitude and the normalized difference vegetation index (NDVI). The distribution patterns for plateau pikas and plateau zokors were driven by HFI and NDVI. Climate has played a substantial role in shaping suitable habitats for these three Glires on the QTP. Their suitable area is expected to decrease over the next 30-50 years, along with their niche breadth and overlap. Future suitable habitats for the three Glires tended to shift toward higher latitudes on the QTP.

CONCLUSION

These findings underscore the impacts of environmental and human factors on the distribution of the three Glires on the QTP. They have enhanced our understanding of the intricate relationships between Glires niches and environments. This can aid in identifying necessary interventions for developing effective early warning systems and prevention strategies to mitigate Glires infestations and plague epidemics on the QTP. © 2024 Society of Chemical Industry.

Multi-Omics Analysis Reveals Dietary Fiber's Impact on Growth, Slaughter Performance, and Gut Microbiome in Durco × Bamei Crossbred Pig

Dietary fiber (DF) is an important nutrient component in pig's diet that remarkably influences their growth and slaughter performance. The ability of pigs to digest DF depends on the microbial composition of the intestinal tract, particularly in the hindgut. However, studies on how DF alters the growth and slaughter performance of pigs by shaping the gut microbial composition and metabolites are still limited. Therefore, this study aimed to investigate the effects of DF on microbial composition, functions, and metabolites, ultimately altering host growth and slaughter performance using Durco × Bamei crossbred pigs supplemented with 0%, 10%, 17%, and 24% broad bean silage in the basic diet. We found that the final weight, average daily gain, fat, and lean meat weight significantly decreased with increasing DF. Pigs with the lowest slaughter rate and fat weight were observed in the 24% fiber-supplemented group. Gut microbial communities with the highest alpha diversity were formed in the 17% fiber group. The relative abundance of fiber-degrading bacteria, bile acid, and succinate-producing bacteria, including Prevotella sp., Bacteroides sp., Ruminococcus sp., and Parabacteroides sp., and functional pathways, including the butanoate metabolism and the tricarboxylic acid [TCA] cycle, significantly increased in the high-fiber groups. The concentrations of several bile acids significantly decreased in the fiber-supplemented groups, whereas the concentrations of succinate and long-chain fatty acids increased. Our results indicate that a high-fiber diet may alter the growth and slaughter performance of Durco × Bamei crossbred pigs by modulating the composition of Prevotella sp., Bacteroides sp., Ruminococcus sp., Parabacteroides sp., and metabolite pathways of bile acids and succinate.

Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles

Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.

Effects of Freshwater Acidification on the Gut Microbial Community of Trachemys scripta elegans

Freshwater acidification (FA) has become a global environmental problem, posing a potential threat to freshwater ecosystems. The gut microbiota plays a crucial role in the host's response and adaptation to new environments. In this study, we investigated the changes in microbial communities in Red-eared slider (Trachemys scripta elegans) under acidic conditions to reveal the ecological impacts of acidification on freshwater turtles. The results showed that there were significant differences in β-diversity (p = 0.03), while there were no significant differences in the α-diversity of gut microbiota in T. s. elegans between the different levels of acidification (pH of 5.5, 6.5, 7.5). Both the Gut Microbiome Health Index (GMHI) and the Microbial Dysbiosis Index (MDI) exhibited significant differences when comparing environments with a pH of 5.5 to those with a pH of 6.5 (p < 0.01). A comparative analysis between pH levels of 5.5 and 6.5 also revealed substantial differences (p < 0.01). Likewise, a comparative analysis between pH levels of 6.5 and 7.5 also revealed substantial differences (p < 0.01). At the phylum level, Firmicutes, Fusobacteria, and Bacteroidota formed a major part of the gut microbial community, Fusobacteria showed significant differences in different acidity environments (p = 0.03). At the genus level, Cetobacterium, Turicibacter, unclassified Eubacteriaceae, and Anaerorhabdus_furcosa_group showed significant differences in different acidity environments. The pH reduced interactivity in the gut microbiota of T. s. elegans. In addition, LEfSe analysis and functional prediction revealed that the potentially_pathogenic and stress_tolerant functional characteristics also showed significant differences in different acidity environments. The findings underscore the pivotal role of the gut microbiota in T. s. elegans in response to freshwater acidification and provide a foundation for further exploration into the impacts of acidification on freshwater ecosystems.

Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas

IMPORTANCE

The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.

Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas (Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.

Male infertility risk and gut microbiota: a Mendelian randomization study

Background

In recent decades, the decline of male sperm quality has become a worldwide phenomenon, with sperm quality of critical importance for the ability to conceive naturally. Recent studies suggest that male fertility function is closely linked to the gut microbiota, however, the cause-and-effect association between the gut microbiota and male infertility risk is currently unclear.

Methods

We performed one two-sample Mendelian randomization (MR) study, which uses summary data on human gut microbiota from the MiBioGen consortium as factors of exposure. FinnGen Consortium R8 data was used to obtain GWAS data for male infertility. To evaluate cause-and-effect associations linking gut microbiota and male infertility risk with multiple Mendelian randomization methods, we included inverse variance weighted (IVW), MR-Egger, and Maximum Likelihood (ML) Ratio. The heterogeneity of instrumental variables was evaluated through Cochran's Q, Rucker's Q, and leave-one-out analysis methods.

Results

We found a positive association between Allisonella, Anaerotruncus, Barnesiella, Intestinibacter, and Lactococcus with male infertility risk according to the MR analysis results. Bacteroides Romboutsia, Ruminococcaceae (NK4A2140group), and Ruminococcaceae (UCG011) play a protective function in male infertility pathogenesis.

Conclusion

It was found that gut microbiota and infertility are causally related in this study. In subsequent studies, there is a need to build a larger and more comprehensive GWAS database on male infertility, which will reveal the underlying mechanisms for gut microbiota and male infertility. There is a need for randomized controlled trials for validating the protective effect of the associated gut microbiota against male infertility risk, and for exploring the associated mechanisms.