Comparison of Bacterial and Fungal Community Structure and Potential Function Analysis of Yak Feces before and after Weaning

Analysis of the microbial diversity in the fecal material of the critically endangered orangutan

The orangutan ( Pongo spp.) is a critically endangered species. Today, populations of these animals are rapidly declining by up to 75%. They are found in the tropical rainforests of Borneo and Sumatra. In this study, using a next generation sequencing approach, the bacterial and fungal diversity in the fecal material of orangutans living in the Racine Zoo were investigated. The most predominant bacterial phyla were the Bacillota along with Bacteroidota. The most predominant fungal phylum was Ascomycota. Finally, the various functions of the bacterial communities present in the fecal material were predicted with PICRUSt2 using the KEGG database.

Effect of differences in residual feed intake on gastrointestinal microbiota of Dexin fine-wool meat sheep

In this study, we examined the effects of different residual feed intakes (RFIs) on nutrient digestibility and the microbiota of the digestive tract of Dexin fine-wool sheep. Fifty 70-day-old Dexin fine-wool meat lambs were selected as the experimental group and fed in a single pen for 100 days. Based on their mid-term metabolic weight, 100-day average daily weight gain and daily feed intake, the male Dexin lambs were divided into a low-RFI group (13), a mid-RFI group (18), and a high-RFI group (11). Six male Dexin lambs were selected from each group to collect feces, rumen digesta and solid digesta. Rectal feces were collected from three lambs in each group. The results showed that the digestibility of dry matter and crude protein by sheep in the L-RFI group was than that in the H-RFI group (P < 0.05). Within the microbial population, f_Anaerovoracaceae, g_Christensenellaceae_R_7_group, p_Proteobacteria, and g_Roseburia were significantly correlated with RFI. Energy metabolism, metabolism of amino acids and carbohydrates, transport and catabolism, and cell migration pathways were upregulated in the L-RFI group. The differences in the microbiota of the digestive tract of sheep with different RFIs were reflected in the presence of some key bacterial genera rather than changes in the overall microbial diversity.

Sex-Induced Changes in Microbial Eukaryotes and Prokaryotes in Gastrointestinal Tract of Simmental Cattle

This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics were assessed, revealing significant differences in the diversity and composition of archaeal communities between males and females. Notably, females exhibited higher alpha diversity in archaea, while beta diversity analyses indicated distinct clustering of bacterial and archaeal communities by gender. The study also identified correlations between specific microbial taxa and hematological parameters, with Treponema and Methanosphaera showing gender-specific associations that may influence cattle health and productivity. These findings highlight the importance of considering gender in microbiota-related research and suggest that gender-specific management strategies could optimize livestock performance. Future research should explore the role of sex hormones in shaping these microbial differences.

Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.

Parasitism-Induced Changes in Microbial Eukaryotes of Peruvian Alpaca Gastrointestinal Tract

Alpacas, important genetic resources in the Andean region of Peru, are vulnerable to diarrhea caused by pathogenic parasites such as Eimeria lamae and Giardia sp., which can be fatal, especially in neonates, due to their physiological immaturity and limited adaptability. The study investigated the diversity and abundance of intestinal fungi and protists in alpacas infected with Eimeria lamae and Giardia sp. compared to healthy alpacas. A total of 19 alpacas, aged between one and two months, were included. They were divided into two groups, one with pathological conditions (nine) and the other healthy (ten). Parasitological analyses for the detection of parasites and subsequent molecular analysis were performed on the collected fecal samples. The results revealed a greater diversity and abundance of protists in infected alpacas in comparison with healthy alpacas, while the fungal composition did not show significant changes. Therefore, parasitic infections affect the protist component of the alpaca gut microbiota. Also, it was observed that Blastocystis was identified in all healthy alpacas, serving as a possible marker of the health of the intestinal microbiota; in addition, Prussia and Pichia are beneficial fungi that help control diseases. This groundbreaking study in neonatal alpacas is the first to explore potential changes in the intestinal microbiota during an infectious state, underscoring the importance of further research to comprehend its effects on alpaca health and immune responses.

Comparative analysis of endophytic fungal communities in bamboo species Phyllostachys edulis, Bambusa rigida, and Pleioblastus amarus

Fungal endophytes in plant leaf mesophyll form mutually beneficial associations through carbon assimilation, synthesis of biologically active chemicals, and enhancement of aesthetic and nutritional value. Here, we compared community structure, diversity, and richness of endophytic fungi in the leaves of three bamboo species, including Phyllostachys edulis (MZ), Bambusa rigida (KZ), and Pleioblastus amarus (YT) via high-throughput Illumina sequencing. In total, 1070 operational taxonomic units (OTUs) were retrieved and classified into 7 phylum, 27 classes, 82 orders, 185 families, 310 genus, and 448 species. Dominant genera were Cladosporium, Trichomerium, Hannaella, Ascomycota, Sporobolomyces, Camptophora and Strelitziana. The highest fungal diversity was observed in Pleioblastus amarus, followed by Bambusa rigida, and Phyllostachys edulis. Comparatively, monopodial species Ph. edulis and sympodial B. rigida, mixed P. amarus revealed the highest richness of endophytic fungi. We retrieved a few biocontrol agents, Sarocladium and Paraconiothyrium, and unique Sporobolomyces, Camptophora, and Strelitziana genera. FUNGuild analysis revealed the surrounding environment (The annual average temperature is between 15 and 25 °C, and the relative humidity of the air is above 83% all year round) as a source of fungal accumulation in bamboo leaves and their pathogenic nature. Our results provide precise knowledge for better managing bamboo forests and pave the way for isolating secondary metabolites and potential bioactive compounds.

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies' (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

Synergistic Effect of Yak Dung Fiber and Yak Dung Ash on the Mechanical and Shrinkage Properties of Cement Mortar

The high value use of agricultural and livestock waste resources in the context of a low carbon economy is a challenge that currently plagues many countries. Yak dung, as a waste resource from livestock farming in the plateau, is considered to be a misplaced treasure. In this work, yak dung was processed into yak dung fiber (YDF) and yak dung ash (YDA), respectively, and the microscopic morphology of the YDF and YDA was assessed using scanning electron microscopy (SEM). The elements in the YDA were analyzed by energy dispersive X-ray spectroscopy (EDX). Moreover, cementitious composites were prepared with YDF at 0%, 0.3%, 0.5% and 0.7% and by replacing cement with YDA at 5%, 10% and 15% to assess the workability, mechanical properties and shrinkage properties of cementitious composites containing different YDF types (alkali treated and untreated), contents and different YDA contents. The results showed that alkali-treated YDF and YDA contain a large number of honeycomb structure pores, and the strength of cementitious materials with alkali-treated YDF was higher. The addition of YDF had a negative effect on the fluidity and compressive strength of the cementitious material, but the 0.3% YDF was beneficial in increasing its flexural strength. The compressive strength and flexural strength first increased and then decreased with the increase of YDA content. Both YDF and YDA inhibited the shrinkage of the cement paste, and the shrinkage strain of the cement matrix composites containing 0.3% YDF and 10% YDA was reduced by 51.1% compared to the control group. This work is expected to promote the application of yak dung waste in cementitious materials.