Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas

Impact of Panax notoginseng Residue on Rumen Microbial Community, Blood Biochemical Parameters and Growth Performance in Cattle: A Preliminary Study on Its Potential as a Feed Resource

This study aimed to investigate the effects of adding different proportions of Panax notoginseng residue (PNR) to the diet on the rumen microbial community structure, blood biochemical indices, and growth performance of Wenshan cattle. Fifteen Wenshan cattle with an average weight of 392.30 ± 22.57 kg were randomly divided into three groups, a control group, a 3% PNR group, and a 6% PNR group, with five cattle in each group, for a 100-day feeding trial. The results show that adding PNR to the diet modulates the abundance and diversity of rumen microorganisms in Wenshan cattle, primarily affecting the relative abundances of key bacterial phyla such as Firmicutes, Proteobacteria, and Bacteroidetes. At the genus level, the relative abundances of Fibrobacter and Butyrivibrio exhibited trends of either decreasing and then increasing or increasing then decreasing with the amount of PNR added, indicating a complex regulatory effect of PNR on the rumen microbial community. The addition of PNR decreased blood glucose and blood lipid levels in Wenshan cattle. Moreover, PNR addition also increased the average daily weight gain of Wenshan cattle, demonstrating its positive effect on enhancing growth performance. In summary, PNR, as a feed resource, has potential application value in the feeding of Wenshan cattle. It not only regulates the rumen microbial community structure and improves metabolic health but also effectively enhances animal growth performance.

Composition, Influencing Factors, and Effects on Host Nutrient Metabolism of Fungi in Gastrointestinal Tract of Monogastric Animals

Intestinal fungi, collectively referred to as mycobiota, constitute a small (0.01-2%) but crucial component of the overall intestinal microbiota. While fungi are far less abundant than bacteria in the gut, the volume of an average fungal cell is roughly 100-fold greater than that of an average bacterial cell. They play a vital role in nutrient metabolism and maintaining intestinal health. The composition and spatial organization of mycobiota vary across different animal species and are influenced by a multitude of factors, including age, diet, and the host's physiological state. At present, quantitative research on the composition of mycobiota in monogastric animals remains scarce, and investigations into the mechanisms underlying their metabolic functions are also relatively restricted. This review delves into the distribution characteristics of mycobiota, including Candida albicans, Saccharomyces cerevisiae, Kazachstania slooffiae, in monogastric animals, the factors influencing their composition, and the consequent impacts on host metabolism and health. The objective is to offer insights for a deeper understanding of the nutritional significance of intestinal fungi in monogastric animals and to explore the mechanisms by which they affect host health in relation to inflammatory bowel disease (IBD), diarrhea, and obesity. Through a systematic evaluation of their functional contributions, this review shifts our perception of intestinal fungi from overlooked commensals to key components in gut ecosystem dynamics, emphasizing their potential in personalized metabolic control regulation and the enhancement of disease prevention and treatment strategies.

Captivity increased the abundance of high-risk antibiotic resistance genes in the giant panda gut microbiome

Captivity is a key strategy for protecting endangered species, but research has primarily focused on artificial breeding and reintroduction to bolster wild populations, often overlooking the environmental and health risks associated with antibiotic resistance genes (ARGs). Here, we conducted a comprehensive analysis of the microbiome and ARG profiles in the gut of wild giant pandas across five representative populations, as well as one captive population, utilizing 16S rRNA gene sequencing and High-Throughput Quantitative PCR. Our findings revealed that both geographic location and captivity significantly influenced the gut microbial community and ARG composition in the gut of giant pandas. Additionally, we identified core microbiomes with essential ecological functions, particularly those related to food utilization, were identified in the giant panda gut across different regions. The gut ARGs in giant pandas exhibited a broad range of subtypes, with multidrug resistance genes being the most prevalent. Notably, the captive population harbored the highest abundance of high-risk ARGs, especially those conferring tetracycline resistance. High-risk multidrug ARGs (e.g., tolC, mepA, and mdtA) were found to be strongly correlated with the potential pathogens, such as Escherichia_Shigellina and Pseudomonas. Furthermore, bamboo-associated ARGs and mobile genetic elements (MGEs) contributed significantly to the ARG abundance in the giant panda gut, indicating that diet plays a crucial role in shaping gut resistome. Collectively, our study provides a detailed mapping of giant panda gut microbiomes and ARG distribution, offering valuable insights for conservation efforts and advancing our understanding of ARG dynamics in giant panda populations.

Seasonal Changes and Age-Related Effects on the Intestinal Microbiota of Captive Chinese Monals (Lophophorus lhuysii)

The Chinese monal (Lophophorus lhuysii) is a large-sized and vulnerable (VU in IUCN) bird from southwestern China. This study applied 16S rRNA high-throughput sequencing to comprehensively examine the gut microbiota of captive Chinese monals (located in Baoxing, Sichuan, China) across varying seasons and life stages. Dominant bacterial phyla identified included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Significant seasonal and age-associated shifts were observed within specific bacterial groups, particularly marked by seasonal fluctuations in beta diversity. Moreover, linear discriminant analysis effect size (LEfSe) and functional predictions highlighted distinct winter signatures, indicating possible functional shifts in energy metabolism and disease resistance. In mid-aged adults, an expansion of Gamma-Proteobacteria suggested an elevated susceptibility of the gut microbiota of Chinese monals to chronic disorders and microbial imbalance. Putative pathogenic bacteria exhibited increased abundance in spring and summer, likely driven by temperature, host physiological cycles, interspecies interactions, and competition. These findings imply that the diversity, and structure of the gut microbiota in captive Chinese monals are strongly influenced by seasonal and age-related factors. The insights provided here are essential for improving breeding strategies and preventing gastrointestinal diseases in captivity.

Limited gut bacterial response of tuatara (Sphenodon punctatus) to dietary manipulation and captivity

The bacteria of a host's digestive tract play crucial roles in digestion and pathogen resistance. Hosts living in captivity often have more human interaction and antibiotic use, in addition to differences in diet and environment, compared to their wild counterparts. Consequently, wild and captive animals frequently harbour different bacterial communities. We tested whether diversity of diet provided in captivity shifts the gut bacteria of tuatara, an endemic New Zealand reptile, at three captive sites, and examined how the gut community of these tuatara compares to those in the wild. Dietary manipulation did not cause a strong overall shift in tuatara gut bacteria, but individual tuatara did experience bacterial shifts during manipulation, which subsequently reverted after manipulation. We found that Bacteroides, a genus common in most vertebrate guts but rare in tuatara, increased significantly in the gut during manipulation, then decreased post-manipulation. Finally, the gut bacteria of captive tuatara significantly differed from those of wild tuatara, though most of the dominant bacterial genera found in wild tuatara persisted in captive tuatara. This work represents a first investigation of the captive tuatara bacterial community and establishes the sensitivity of the gut community to dietary manipulation and captivity for this relict reptile.

Nutrient Utilization and Gut Microbiota Composition in Giant Pandas of Different Age Groups

Proper feeding and nutrition are vital for maintaining the health of giant pandas (GPs), yet the impact of dietary changes and gut microbiota on their nutrient utilization remains unclear. To address these uncertainties, we investigated nutrient intake and apparent digestibility, as well as gut microbiota composition across different age groups of giant pandas: sub-adults (SGPs), adults (AGPs), and geriatrics (GGPs). Our findings revealed notable shifts in dietary patterns from SGPs to GGPs. As they aged, significantly more bamboo shoots and less bamboo were consumed. Consequently, GGPs showed significantly reduced crude fiber (CF) intake and digestibility, while crude protein (CP) did not alter significantly. In addition, 16S rRNA microbial sequencing results showed that unidentified_Enterobacteriaceae and Streptococcus were the dominant genera among all age groups. The relative abundance of the genus Enterococcus in GGPs was significantly higher than that in SGPs and AGPs (p < 0.05). Overall, our results indicated the importance of bamboo shoots as a major source of protein in GGPs' diet, which can effectively compensate for the certain nutritional loss caused by the reduction in bamboo intake. Age-related changes in bacterial abundance have an effect on specific nutrient apparent digestibility in the gut of GPs. The data presented in this study serve as a useful reference for nutritional management in different ages of GPs under healthy conditions.

Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome

Introduction

The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages.

Methods

In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes.

Results

The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways.

Discussion

This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda (Ailuropoda melanoleuca)

Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism.

IMPORTANCE

Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.

Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand

Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.

Gastrointestinal microbiome, resistance genes, and risk assessment of heavy metals in wild giant pandas

The gastrointestinal microbiome (GM) of giant panda (GP) plays an important role in food utilization and health and is also an essential reservoir of resistance genes. Currently, little knowledge is available on the GM, acid resistance genes (AcRGs), antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in wild GPs. We sampled the gastrointestinal tract of a dead GP and explored the composition and function of GM and resistance genes through cryo-scanning electron microscopy, metagenomic sequencing, and genome-resolved metagenomics. The concentration of metals in the gastrointestinal lumen, feces, bamboo, and soil was measured by inductively coupled plasma mass spectrometry. Results showed that the composition of the microbiota varied in different gastrointestinal regions. Fecal microbiota was highly associated with small intestinal and colonic microbes. The lignocellulosic cross-linked structure of bamboo was destroyed in the stomach initially and destroying degree increased from stomach to anus. Reconstruction of metagenome-assembled-genomes confirmed that core GM, e.g., Streptococcus, Clostridium, Lactococcus, Leuconostoc, and Enterococcus, carried genes encoding the lignocellulose degradation enzyme. There were no significant differences of resistance genes between gastrointestinal and fecal samples, except MGEs. Multidrug and multi-metal resistance genes were predominant in all samples, while the transposase gene tnpA was the major type of MGE. Significant correlations were observed among the abundance of GM, resistance genes, and MGEs. Gastrointestinal and fecal mercury and chromium were the main metals influencing GM and resistance genes. The content of gastrointestinal and fecal metals was significantly associated with the presence of the same metals in bamboo, which could pose a threat to the health of wild GPs. This study characterized the gastrointestinal microbiome of wild GPs, providing new evidence for the role of the gastrointestinal microbiome in degrading lignocellulose from bamboo and highlighting the urgent need to monitor metal levels in soil and bamboo.

Gut microbiota bridges dietary nutrients and host immunity

Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.

16S rRNA gene-based meta-analysis of the reptile gut microbiota reveals environmental effects, host influences and a limited core microbiota

An animal's gut microbiota plays an important role in host health, reproduction and digestion. However, many studies focus on only a few individuals or a single species, limiting our ability to recognize emergent patterns across a wider taxonomic grouping. Here, we compiled and reanalysed published 16S rRNA gene sequence data for 745 gut microbiota samples from 91 reptile species using a uniform bioinformatics pipeline to draw broader conclusions about the taxonomy of the reptile gut microbiota and the forces shaping it. Our meta-analysis revealed the significant differences in alpha- and beta-diversity across host order, environment, diet, habitat and conservation status, with host diet and order contributing the most to these differences. We identified the principal bacterial phyla present in the reptile gut microbiota as Bacteroidota, Proteobacteria (mostly Gamma class), and Firmicutes, and detected the bacterial genus Bacteroides in most reptile individuals, thus representing a putative 'core' microbiota. Our study provides novel insights into key drivers of the reptile gut microbiota, highlights existing knowledge gaps and lays the groundwork for future research on these fascinating hosts and their associated microbes.

Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure

Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.

Metabolic Fate of Lignin in Birch Glucuronoxylan Extracts as Dietary Fiber Studied in a Rat Model

SCOPE

While previously considered inert, recent studies suggest lignin metabolism with unknown metabolic fates is occurring in the gastrointestinal tract of several animal models. This study focuses on analyzing the potential metabolites of lignin.

METHODS AND RESULTS

The diets of rats include relatively pure birch glucuronoxylan (pureGX) with residual lignin or lignin-rich GX (GXpoly) in their diet. Nuclear magnetic spectroscopy of the lignin isolated from the GXpoly-fed rats fecal sample shows high alteration in chemical structure, whereas lignin-carbohydrate complexes (LCCs) are enriched in fecal samples from the pureGX group. Moreover, the increased syringyl-to-guaiacyl (S/G) ratio suggests that lignin G-units are predominantly metabolized based on pyrolysis gas chromatography-mass spectrometry (pyr-GC/MS). The presence of small phenolic metabolites identified in urine samples of the GXpoly group, for example, ferulic and sinapic acids, their sulfate and glucuronide derivatives, and 4-sulfobenzylalcohol, suggests that the small fragmented lignin metabolites in the large intestine enter the plasma, and are further processed in the liver. Finally, the relative abundances of polyphenol-degrading Enterorhabdus and Akkermansia in the gut microbiota are associated with lignin metabolism.

CONCLUSION

These findings give further evidence to lignin metabolism in the gut of nonruminants and provide insight to the potential microbes and metabolic routes.

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.

Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas

We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas (Ailuropoda melanoleuca) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium, Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium. Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda's specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.

Captivity restructures the gut microbiota of François' langurs (Trachypithecus francoisi)

Gut microbiota is crucial to primate survival. Data on the gut microbiota of captive and wild animals can provide a physiological and ecological basis for the conservation of rare and endangered species. To study the effect of captivity on the gut microbiota, we examine the difference in the gut microbiota composition between captive and wild Francois' langurs (Trachypithecus francoisi), using 16S rRNA sequencing technology. The results showed that the composition of the gut microbiota of captive and wild langurs was characterized by Firmicutes (51.93 ± 10.07% vs. 76.15 ± 8.37%) and Bacteroidetes (32.43 ± 10.00% vs. 4.82 ± 1.41%) at the phylum level and was characterized by Oscillospiraceae (15.80 ± 5.19% vs. 30.21 ± 4.87%) at the family level. The alpha diversity of gut microbiota in captive langurs was higher than those in wild, such as the Shannon index (4.45 ± 0.33 vs. 3.98 ± 0.19, P < 0.001) and invSimpson index (35.11 ± 15.63 vs. 19.02 ± 4.87, P < 0.001). Principal coordinates analysis (PCoA) results showed significant differences in the composition of gut microbiota between captive and wild langurs at both the phylum and family levels (weight UniFrac algorithm, phylum level: R² = 0.748, P = 0.001; family level: R² = 0.685, P = 0.001). The relative abundance of Firmicutes (51.93 ± 10.07%) in captive langurs was lower than that of wild langurs (76.15 ± 8.37%), and the relative abundance of Bacteroidetes (32.43 ± 10.00%) in captive langurs was higher than that of wild (4.82 ± 1.41%). Our study concludes that dietary composition could be a crucial determinant in shaping the gut microbiota of langurs because more fiber-rich foods used by the wild langurs could increase the abundance of Firmicutes, and more simple carbohydrate-rich foods consumed by the captive langurs increase the abundance of Bacteroidetes. We highlight the importance of captivity on the gut microbiota and the need to consider the gut microbiota in animal provision.

Seasonal variations in the gut microbiota of white-headed black langur (Trachypithecus leucocephalus) in a limestone forest in Southwest Guangxi, China

Investigating gut microbiota is important for understanding the physiological adaptation of animals to food availability changes in fragmented habitats and consequently providing new ideas for the conservation of endangered wild animals. In this study, we explored the gut microbiota of the endangered white-headed black langur (Trachypithecus leucocephalus), which is endemic to the limestone forests of Southwest Guangxi, China, to understand its adaptation strategies to seasonal changes in habitat using 16S rRNA sequencing. Our results revealed significant seasonal variations in the gut microbiota of white-headed black langurs. In particular, the alpha diversity was higher in the rainy season than in the dry season, and the beta diversity was significantly different between the two seasons. At the phylum level, the relative abundance of Firmicutes, Actinobacteriota, and Proteobacteria was higher in the dry season than that in the rainy season, whereas that of Bacteroidetes, Spirochaetota, and Cyanobacteria was significantly higher in the rainy season than that in the dry season. At the family level, Oscillospiraceae and Eggerthellaceae were more abundant in the dry season than in the rainy season, whereas Lachnospiraceae, Ruminococcaceae, and Monoglobaceae were more abundant in the rainy season than in the dry season. These results could have been obtained due to seasonal changes in the diet of langurs in response to food plant phenology. In addition, the neutral community model revealed that the gut microbiota assembly of these langurs was dominated by deterministic processes and was more significantly affected by ecological factors in the dry season than in the rainy season, which could be linked to the higher dependence of these langurs on mature leaves in the dry season. We concluded that the seasonal variations in the gut microbiota of white-headed black langurs occurred in response to food plant phenology in their habitat, highlighting the importance of microbiota in responding to fluctuating ecological factors and adapting to seasonal dietary changes.

Animal Age Affects the Gut Microbiota and Immune System in Captive Koalas (Phascolarctos cinereus)

Gut microbiota is one of the major elements in the control of host health. However, the composition of gut microbiota in koalas has rarely been investigated. Here, we performed 16S rRNA gene sequencing to determine the individual and environmental determinants of gut microbiota diversity and function in 35 fecal samples collected from captive koalas. Meanwhile, blood immune-related cytokine levels were examined by quantitative reverse transcription-PCR to initially explore the relationship between the gut microbiota and the immune system in koalas. The relative abundance of many bacteria, such as Lonepinella koalarum, varies at different ages in koalas and decreases with age. Conversely, Ruminococcus flavefaciens increases with age. Moreover, bacterial pathways involved in lipid metabolism, the biosynthesis of other secondary metabolites, and infectious disease show a significant correlation with age. Age affects the relationship between the microbiota and the host immune system. Among them, the gut microbiota of subadult and aged koalas was closely correlated with CD8β and CD4, whereas adult koalas were correlated with CLEC4E. We also found that sex, reproductive status, and living environment have little impact on the koala gut microbiota and immune system. These results shed suggest age is a key factor affecting gut microbiota and immunity in captive koalas and thus provide new insight into its role in host development and the host immune system. IMPORTANCE Although we have a preliminary understanding of the gut microbiota of koalas, we lack insight into which factors potentially impact captive koalas. This study creates the largest koala gut microbiota data set in China to date and describes several factors that may affect gut microbiota and the immune system in captive koalas, highlighting that age may be a key factor affecting captive koalas. Moreover, this study is the first to characterize the correlation between gut microbiota and cytokines in koalas. Better treatment strategies for infectious disorders may be possible if we can better understand the interactions between the immune system and the microbiota.

Factors shaping the gut microbiome of five species of lizards from different habitats

Background

Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota.

Methods

In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA.

Results

Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards' gut microbiota.

Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.

Diet-induced microbial adaptation process of red deer (Cervus elaphus) under different introduced periods

Insufficient prey density is a major factor hindering the recovery of the Amur tiger (Panthera tigris altaica), and to effectively restore the Amur tiger, red deer (Cervus elaphus) was released into the Huangnihe National Nature Reserve of Northeast China as the main reinforcement. Differences in feeding and synergistic changes caused by the intestinal microbial communities could impact the adaptation of wildlife following reintroductions into field environments. We analyzed the foraging changes in shaping the intestinal microbial community of the red deer after being released to the Huangnihe National Nature Reserve and screened the key microbial flora of the red deer when processing complex food resources. The feeding and intestinal microbial communities of the red deer were analyzed by plant Deoxyribonucleic acid (DNA) barcoding sequencing and 16S rRNA high-throughput sequencing, respectively. The results showed that there were significant differences in food composition between wild and released groups [released in 2019 (R2): n = 5; released in 2021 (R0): n = 6]; the wild group fed mainly on Acer (31.8%) and Abies (25.6%), R2 fed mainly on Betula (44.6%), R0 had not formed a clear preferred feeding pattern but had certain abilities to process and adapt to natural foods. Firmicutes (77.47%) and Bacteroides (14.16%) constituted the main bacterial phylum of red deer, of which, the phylum Firmicutes was the key species of the introduced red deer for processing complex food resources (p < 0.05). The wild release process significantly changed the intestinal microbial structure of the red deer, making it integrate into the wild red deer. The period since release into the wild may be a key factor in reshaping the structure of the microbial community. This study suggested that the intestinal microbial structure of red deer was significantly different depending on how long since captive deer has been translocated. Individuals that have lived in similar environments for a long time will have similar gut microbes. This is the adaption process of the wildlife to natural environment after wild release, taking into account the gut microbes, and the feeding changes in shaping microbial communities can help introduced red deer match complex food resources and novel field environments.

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats

Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.

Wild and Captive Environments Drive the Convergence of Gut Microbiota and Impact Health in Threatened Equids

To explore how the living environment influences the establishment of gut microbiota in different species, as well as the extent to which changes in the living environment caused by captive breeding affect wildlife’s gut microbiota and health, we used 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing to compare the gut microbiome of two species of threatened equids, the Przewalski’s Horse and the Asian wild ass, in the wild and captivity. The results revealed that different species of Equidae living in the same environment showed remarkable convergence of gut microflora. At the same time, captive populations exhibited significantly “unhealthy” microbiota, such as low Alpha diversity, high levels of potentially pathogenic bacteria and biomarkers of physical or psychological disease, and enrichment of microbial functions associated with exogenous exposure and susceptibility, implying that the artificial environment created by captivity may adversely impact the health of wildlife to some extent. Our findings demonstrate the importance of the environmental factors for the establishment of gut microbiota and host health and provide new insights into the conservation of wildlife in captivity from the perspective of the microbiome.

Comparative Analysis of Intestinal Microflora Between Two Developmental Stages of Rimicaris kairei, a Hydrothermal Shrimp From the Central Indian Ridge

Despite extreme physical and chemical characteristics, deep-sea hydrothermal vents provide a place for fauna survival and reproduction. The symbiotic relationship of chemotrophic microorganisms has been investigated in the gill of Rimicaris exoculata, which are endemic to the hydrothermal vents of the Mid-Atlantic Ridge. However, only a few studies have examined intestinal symbiosis. Here, we studied the intestinal fauna in juvenile and adult Rimicaris kairei, another species in the Rimicaris genus that was originally discovered at the Kairei and Edmond hydrothermal vent fields in the Central Indian Ridge. The results showed that there were significant differences between juvenile and adult gut microbiota in terms of species richness, diversity, and evenness. The values of Chao1, observed species, and ASV rarefaction curves indicated almost four times the number of species in adults compared to juveniles. In juveniles, the most abundant phylum was Deferribacterota, at 80%, while in adults, Campilobacterota was the most abundant, at 49%. Beta diversity showed that the intestinal communities of juveniles and adults were clearly classified into two clusters based on the evaluations of Bray-Curtis and weighted UniFrac distance matrices. Deferribacteraceae and Sulfurovum were the main featured bacteria contributing to the difference. Moreover, functional prediction for all of the intestinal microbiota showed that the pathways related to ansamycin synthesis, branched-chain amino acid biosynthesis, lipid metabolism, and cell motility appeared highly abundant in juveniles. However, for adults, the most abundant pathways were those of sulfur transfer, carbohydrate, and biotin metabolism. Taken together, these results indicated large differences in intestinal microbial composition and potential functions between juvenile and adult vent shrimp (R. kairei), which may be related to their physiological needs at different stages of development.

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas

Seasonal variations in gut microbiota of small mammals and how it is influenced by environmental variables is relatively poorly understood. We sampled 162 wild plateau pikas (Ochotona curzoniae) in four seasons over two and a half years and recorded the air temperature, precipitation, and nutrient content in edible vegetation at the sampling site. After conducting 16S rRNA and shotgun metagenomic sequencing, we found that the highest alpha diversity, the relative abundance of Firmicutes, and the simplest co-occurrence network occurred in winter, whereas that the highest relative abundance of Proteobacteria and the most complex network structure was observed in spring. The highest relative abundance of Verrucomicrobiota and Spirochaetota were seen in summer and autumn, respectively. Air temperature, precipitation, and the contents of crude protein, crude fiber, and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota. Diet contributed more to microbial variation than climatic factors. Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer, while abundance of carbohydrate-binding modules and carbohydrate esterases were highest in spring. These microbial variations were related to the changes in dietary nutrition, indicating that gut microbiota of plateau pika contribute to the efficient use of food resources. This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals. This article is protected by copyright. All rights reserved.

Differences in Diet and Gut Microbiota Between Lactating and Non-lactating Asian Particolored Bats (Vespertilio sinensis): Implication for a Connection Between Diet and Gut Microbiota

In mammals, lactation is considered the most energetically costly phase for females. To meet nutritional and energy demands, lactating females usually change feeding patterns by eating food that is higher in protein and calories. Their gut microbes respond accordingly to help adapt to the changes in diet. In this study, we examined differences in diet and gut microbial composition between lactating and non-lactating Asian particolored bats (Vespertilio sinensis) using COI and 16S amplicon sequencing. When compared with non-lactating bats, we found that the diversity and composition of lactating bats' diets differed; the proportion of Diptera increased and Coleoptera and Orthoptera decreased significantly. This could be attributed to the easy availability and high protein content of Diptera. Comparative analysis of the gut microbiota of lactating and non-lactating females showed that although the diversity of gut microbiota did not change, the relative abundance of specific gut microbiota associated with a particular diet did change. For example, when the consumption of Coleoptera decreased in lactating bats, the relative abundance of Lactobacillaceae was also reduced. Lactobacillaceae are thought to be involved in the digestion of Coleopteran exoskeletons. This study suggests that during lactation, Asian particolored bats eat a diet that yields higher levels of protein, and at the same time, the abundance of specific gut microbes change to help their hosts adapt to these changes in diet.

Chromosome-Level Genome Assembly of Cyrtotrachelus buqueti and Mining of Its Specific Genes

Background: The most severe insect damage to bamboo shoots is the bamboo-snout beetle (Cyrtotrachelus buqueti). Bamboo is a perennial plant that has significant economic value. C. buqueti also plays a vital role in the degradation of bamboo lignocellulose and causing damage. The genome sequencing and functional gene annotation of C. buqueti are of great significance to reveal the molecular mechanism of its efficient degradation of bamboo fiber and the development of the bamboo industry.

Results: The size of C. buqueti genome was close to 600.92 Mb by building a one paired-end (PE) library and k-mer analysis. Then, we developed nine 20-kb SMRTbell libraries for genome sequencing and got a total of 51.12 Gb of the original PacBio sequel reads. Furthermore, after filtering with a coverage depth of 85.06×, clean reads with 48.71 Gb were obtained. The final size of C. buqueti genome is 633.85 Mb after being assembled and measured, and the contig N50 of C. buqueti genome is 27.93 Mb. The value of contig N50 shows that the assembly quality of C. buqueti genome exceeds that of most published insect genomes. The size of the gene sequence located on chromosomes reaches 630.86 Mb, accounting for 99.53% of the genome sequence. A 1,063 conserved genes were collected at this assembled genome, comprising 99.72% of the overall genes with 1,066 using the Benchmark Uniform Single-Copy Orthology (BUSCO). Moreover, 63.78% of the C. buqueti genome is repetitive, and 57.15% is redundant with long-term elements. A 12,569 protein-coding genes distributed on 12 chromosomes were acquired after function annotation, of which 96.18% were functional genes. The comparative genomic analysis results revealed that C. buqueti was similar to D. ponderosae. Moreover, the comparative analysis of specific genes in C. buqueti genome showed that it had 244 unique lignocellulose degradation genes and 240 genes related to energy production and conversion. At the same time, 73 P450 genes and 30 GST genes were identified, respectively, in the C. buqueti genome.

Conclusion: The high-quality C. buqueti genome has been obtained in the present study. The assembly level of this insect’s genome is higher than that of other most reported insects’ genomes. The phylogenetic analysis of P450 and GST gene family showed that C. buqueti had a vital detoxification function to plant chemical components.