The role of gut archaea in the pig gut microbiome: a mini-review.

The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.

The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host's dietary adaption to bamboo.

BACKGROUND: The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host's dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown. RESULTS: In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n = 322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison of the metagenomes and meta-transcriptomes in 14 feces revealed genes involved in carbohydrate metabolism were lower, but those involved in protein metabolism were greater in abundance and expression in giant pandas compared to those in herbivores and omnivores. Of note, S. alactolyticus was positively correlated to the KEGG modules of essential amino-acid biosynthesis. After being isolated from pandas and gavaged to mice, S. alactolyticus significantly increased the relative abundance of essential amino acids in mice jejunum. CONCLUSIONS: The study highlights the unique protein metabolic profiles in the giant panda's gut microbiome. The findings suggest that S. alactolyticus is an important player in the gut microbiota that contributes to the giant panda's dietary adaptation by more involvement in protein rather than carbohydrate metabolism. Video Abstract.

Archaea: An under-estimated kingdom in livestock animals.

Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.

A high-speed railway network dataset from train operation records and weather data.

High-speed train operation data are reliable and rich resources in data-driven research. However, the data released by railway companies are poorly organized and not comprehensive enough to be applied directly and effectively. A public high-speed railway network dataset suitable for research is still lacking. To support the research in large-scale complex network, complex dynamic system and intelligent transportation, we develop a high-speed railway network dataset, containing the train operation data in different directions from October 8, 2019 to January 27, 2020, the train delay data of the railway stations, the junction stations data, and the mileage data of adjacent stations. In the dataset, weather, temperature, wind power and major holidays are considered as factors affecting train operation. Potential research values of the dataset include but are not limited to complex dynamic system pattern mining, community detection and discovery, and train delay analysis. Besides, the dataset can be used to solve various railway operation and management problems, such as passenger service network improvement, train real-time dispatching and intelligent driving assistance.

Weaning Time Affects the Archaeal Community Structure and Functional Potential in Pigs.

Archaea are considered a "keystone" of the gut microbiome and are linked with the host's energy harvest and health. Although a few studies have investigated the gut archaea in pigs, especially piglets, little is known about the effects of weaning on archaeal structure and function. In this study, we explored the effects of weaning on the longitudinal changes of archaeal composition, diversity, and functional potential in pigs overtime by re-analyzing a recently published metagenomic dataset that included 176 fecal samples collected from commercial pigs on days 7, 14, 21, 28, 35, 70, and 140 after birth. Overall, the richness and diversity of archaeal species showed an increasing trend, and weaning significantly affected the richness of archaeal species. Methanobrevibacter A smithii significantly decreased and was replaced by Methanobrevibacter A sp900769095 within 2 weeks after weaning. For the functional potential, the richness of KEGG KOs increased over time. LEfSe analysis identified 18 KOs, including for example, ko04623 (cytosolic DNA-sensing pathway), ko00500 (starch and sucrose metabolism), and so on, significantly enriched in the weaning pigs, suggesting the involvement of archaea in the piglets' adaptation to the new diet after weaning. Correlation analysis based on Random Forest regression and Pearson correlation showed that archaeal species richness was significantly associated with pig bodyweight on both days 70 and 140. Methanobrevibacter A sp900769095 (R = 0.405, p = 0.040) and Methanobrevibacter A smithii (R = 0.535, p = 0.004) were positively linked with pigs' bodyweight on days 70 and 140, respectively. Our results revealed the dynamic changes of archaeal diversity and functions and demonstrated the effects of weaning on the gut archaea of pigs, suggesting archaea might play essential roles in swine nutrition, metabolism, and growth performance, especially during the critical weaning process.

The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

The value of apolipoprotein E in distinguishing benign and malignant unilateral pleural effusions.

Pleural effusion (PE) remains insurmountable challenge and public health problem, requiring novel noninvasive biomarkers for accurate diagnosis. The aim of this study was to assess the clinical significance of apolipoprotein E (Apo-E) in PE, in order to determine its potential use as a diagnostic biomarker for malignant PE (MPE).PE samples were obtained from 127 patients and the etiology of PE was determined by multiple diagnostic techniques. Apo-E levels were then measured in the pleural fluid samples.58 PE patients were diagnosed with tumors, while 69 were tumor-free. Apo-E levels in MPE patients were significantly higher than those with benign PE (BPE) (P < .05). An Apo-E cut-off of 69.96 ng/mL yielded sensitivity and specificity of 79.31% and 73.91% respectively for MPE detection. The area under the curve for Apo-E was 0.793 (95% confidence interval: 0.712 to 0.860), which was smaller than that of carcinoembryonic antigen (CEA) (Z = 2.081, P<.05). In addition, the combination of Apo-E and CEA detection yielded a higher sensitivity of 87.90% and specificity of 95.65% in diagnosing MPE.In conclusion, Apo-E levels in PE may be a potential biomarker for the detection of MPE. The combined detection of Apo-E and CEA could improve the diagnostic sensitivity and specificity for MPE. These findings provide a simple and convenient method for clinical screening and detection of PE.

Novel heterozygous BPIFC variant in a Chinese pedigree with hereditary trichilemmal cysts.

BACKGROUND: Trichilemmal cysts (TCs) are common intradermal or subcutaneous cysts, which are commonly sporadic and rarely autosomal dominantly inherited. However, little is known about the disease-determining genes in families with TCs exhibiting Mendelian inheritance. OBJECTIVE: The aim of this study was to identify the causative gene in a family with TCs. METHODS: Whole-exome sequencing was performed on a TCs family to identify the candidate gene. Sanger sequencing was conducted to validate the candidate variants and familial segregation. RESULTS: We identified the heterozygous variant c.3G>C (p.Met1?) within the BPIFC gene. Sanger sequencing confirmed the cosegregation of this variant with the TCs phenotype in the family by demonstrating the presence of the heterozygous variant in all the 12 affected and absence in all the seven unaffected individuals. This variant was found to be absent in dbSNP141, 1,000 Genomes database and 500 ethnicity matched controls. CONCLUSION: Our results imply that BPIFC is a causative gene in this Chinese family with hereditary TCs. Further studies should be performed to validate the role of BPIFC in the pathogenesis of this disease.