Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae

Effects of dietary nutrients of the gut microbiota in the long-tailed dwarf hamster (Cricetulus longicaudatus)

Gut microbiota is a key factor in maintaining the dietary and metabolic homeostasis of small mammals. To explore the effect of diet on the gut microbiota of the long-tailed dwarf hamster (Cricetulus longicaudatus), 16S rDNA high-throughput sequencing combined with bioinformatics analysis was used to investigate the succession process of the gut microbiota and effects of different nutrients on the composition and function of the gut microbiota. The results showed that diet structure can significantly influence the composition and function of the gut microbiota, as well as the health of animals. The highest relative abundance of Firmicutes, and the simplest co-occurrence network occurred in the wild. Whereas the relative abundance of Bacteroidetes is higher and the most complex network structure was observed after 35 days of same feeding. Compared to the other four groups, the relative abundance of Firmicutes in the wheat + peanuts (WP) group was the highest after 35 days of different feeding, and the highest relative abundance of Bacteroidetes occurred in the wheat-only (WH) group. Bacteroidetes exhibit carbohydrate degradation activity, and Firmicutes are strongly associated with fat uptake. We also found a significant positive correlation between Lactobacillus and body weight, indicating that Lactobacillus plays a crucial role in modulating fat intake and weight management. This study provides empirical evidence to facilitate the understanding of the co-evolutionary dynamics between C. longicaudatus and their gut microbiota and establishes a theoretical foundation for utilizing gut microbiota in rodent control.

Maternal Malic Acid May Ameliorate Oxidative Stress and Inflammation in Sows through Modulating Gut Microbiota and Host Metabolic Profiles during Late Pregnancy

Sows suffer oxidative stress and inflammation induced by metabolic burden during late pregnancy, which negatively regulates reproductive and lactating performances. We previously found that L-malic acid (MA) alleviated oxidative stress and inflammation and improved reproductive performances in sows. However, the mechanism underlying the MA's positive effects remains unexplored. Here, twenty Large White × Landrace sows with similar parity were randomly divided into two groups and fed with a basal diet or a diet supplemented with 2% L-malic acid complex from day 85 of gestation to delivery. The gut microbiome, fecal short-chain fatty acids, and untargeted serum metabolome were determined. Results showed that Firmicutes, Bacteroidota, and Spirochaetota were the top abundant phyla identified in late pregnancy for sows. Maternal MA supplementation modulated the composition but not the richness and diversity of gut microbiota during late pregnancy. Correlation analysis between gut microbiota and antioxidant capacity (or inflammation indicators) revealed that unclassified_f_Ruminococcaceae, unclassified_f_Lachnospiraceae, UCG-002, norank_f_norank_o_RF3, and Lactobacillus might play a role in anti-oxidation, and Lachnospiraceae_XPB1014_group, Lachnospiraceae_NK4A136_group, UCG-002, unclassified_f_Ruminococcaceae, Candidatus_Soleaferrea, norank_f_UCG-010, norank_f_norank_o_RF39, and unclassified_f_Lachnospiraceae might be involved in the anti-inflammatory effect. The improved antioxidant and inflammation status induced by MA might be independent of short chain fatty acid changes. In addition, untargeted metabolomics analysis exhibited different metabolic landscapes of sows in the MA group from in the control group and revealed the contribution of modified amino acid and lipid metabolism to the improved antioxidant capacity and inflammation status. Notably, correlation results of gut microbiota and serum metabolites, as well as serum metabolites and antioxidant capacity (or inflammation indicators), demonstrated that differential metabolism was highly related to the fecal microorganisms and antioxidant or inflammation indicators. Collectively, these data demonstrated that a maternal dietary supply of MA can ameliorate oxidative stress and inflammation in sows through modulating gut microbiota and host metabolic profiles during late pregnancy.

Black soldier fly pulp in the diet of golden pompano: Effect on growth performance, liver antioxidant and intestinal health

Black soldier fly (Hermetia illucens) has been widely researched as a protein source for fish meal replacement in aquaculture, but few studies have focused on its potential as a feed additive for growth and immune enhancement. We conducted a 56-day culture experiment to determine the impact of feed addition of black soldier fly pulp (BSFP, with 86.2% small peptides in dry basis) on growth performance, plasma biochemistry, liver antioxidant levels, intestinal immunity, digestion and microbiota of juvenile golden pompano (Trachinotus ovatus, 5.63 ± 0.02 g). BSFP was added to the basal diet at 0%, 1%, 3%, 5%, 7% and 9% (named Control, BSFP-1, BSFP-3, BSFP-5, BSFP-7, BSFP-9), respectively. BSFP increased the weight gain rate, specific growth rate, protein efficiency ratio and reduced the feed conversion rate of juvenile T. ovatus, the optimal growth performance was reached at BSFP-1, after which a negative feedback phenomenon was observed. Low levels of BSFP upregulated the expression of hepatic antioxidant, intestinal tight junctions, anti-inflammatory related genes and enhanced antioxidant, immune and intestinal digestive enzyme activities, which simultaneously reduced hepatic malondialdehyde and plasma aspartate transaminase and alanine aminotransferase concentrations. However, at BSFP-7, catalase activity was significantly reduced, while NF-κB p65 and pro-inflammatory cytokines transcription was significantly enhanced (P < 0.05). The results suggest that high doses of BSFP addition may damage fish health by inhibiting small peptide uptake, decreasing the activity of antioxidant enzyme and activating the canonical NF-κB pathway. Conversely, low doses of BSFP enhanced intestinal tight junction protein transcription, digestive enzyme activity and immune performance, inhibited pathogenic microbiota, while enhancing liver antioxidant capacity, which was associated with activated Nrf2-Keap1 pathway and suppressed NF-κB pathway, showing its potential as a feed additive to aquafeeds.

Responses to Reduced Feeding Frequency in Captive-Born Cheetahs (Acinonyx jubatus): Implications for Behavioural and Physiological Stress and Gastrointestinal Health

Unnatural diet composition and frequent feeding regimes may play an aetiological role in the multiple diseases prevalent in captive cheetahs. This study investigated the responses of captive-born (hand-reared) cheetahs (n = 6) to a reduced feeding frequency schedule distinguished by offering larger quantities of food less frequently. The study cheetahs were fed four once-daily meals per week during the 3-week treatment period, followed by a 3-week control period in which they were fed two daily rations six days a week. Total weekly food intake was maintained throughout the study. Variations in behaviour, faecal consistency score (FCS), and faecal glucocorticoid metabolite concentration were measured. Less frequent feeding resulted in higher FCS (p < 0.01) and locomotory behaviour (p < 0.05) among the studied cheetahs. Faecal glucocorticoid metabolite concentration demonstrated an initial acute stress response to the change in feeding frequency (p < 0.05) and subsequent adaptation. The results of the FCS analysis suggest that the more natural feeding pattern could have benefited the studied cheetahs' gastrointestinal health without a significant behavioural or physiological stress response overall to the change in feeding frequency.

Insights into the Gut Microbiota of the Freshwater Crab Sinopotamon planum across Three Seasons and Its Associations with the Surrounding Aquatic Microbiota

Gut microbiota is closely related to the health of the host and its adaptation to environmental changes. Sinopotamon planum is a species of freshwater crab that lives in the water for three seasons and plays a key role in freshwater ecosystems as a benthic macroinvertebrate, an important indicator of aquatic ecological health. In this study, we sequenced 60 gut microbial samples of S. planum and nine microbial samples from the surrounding water in spring, summer, and autumn based on the 16S rRNA gene. The results showed that gut microbiota had the highest alpha diversity in summer, which may be related to increased adaptability in summer. Firmicutes, Proteobacteria, and Bacteroidota were the most dominant phyla of gut microbiota across three seasons, with Candidatus Hepatoplasma and Candidatus Bacilloplasma being the main genera. These main phyla and genera may be key to maintaining a stable function of the intestinal environment. Firmicutes was the phylum with the highest relative abundance, which is probably related to the carnivorous behaviour of S. planum. The abundant C. Hepatoplasma may be related to the starvation of S. planum in the wild. In both gut and water microbiota, beta diversity analyses showed significant differences across seasons. Comparative analysis of gut microbes and surrounding water microbes showed significant differences in microbial diversity and composition between gut and surrounding water. In conclusion, the structure of the gut microbial community of S. planum differed significantly between the studied seasons, but the water microbial community around S. planum was less variable and significantly different from the gut microbes. The seasonal differences in gut microbes are more likely the result of self-internal adaptation to changes in water temperature and food resources between seasons.

Pueraria lobata polysaccharides alleviate neonatal calf diarrhea by modulating gut microbiota and metabolites

Introduction

Neonatal calf diarrhea (NCD) is still one of the most critical diseases in calf rearing. Studies have shown that Pueraria lobata polysaccharides (PLP) have intense antioxidant and immunomodulatory activity and modulate gut microbiota. This randomized clinical trial aimed to determine the effect of PLP on the neonatal calf with diarrhea.

Methods

In this study, we recorded the fecal score of experimental calves, and calves with fecal scores ≥ 2 were determined as diarrhea and assessed their serum concentrations of inflammatory cytokines and oxidative damage-related indices. Fecal microbiota and metabolomics of diarrheal calves were further investigated.

Results

Results showed that treatment with PLP decreased the fecal score of diarrheal calves, serum concentrations of IL-1β, TNF-γ, and malondialdehyde, and also elevated the level of superoxide dismutase. In addition, PLP treatment altered the gut microbiota, significantly increased the relative abundances of beneficial bacteria, including the phyla Bacteroidetes and Actinobacteria, the genus Collinsella, Megamonas, and Bifidobacterium; decreased the relative abundances of pathogenetic or diarrhea related bacteria, such as Proteobacteria, Fusobacteria, Clostridium_sensu_stricto_1, and Escherichia_Shigella. Moreover, PLP can increase the fecal concentrations of isobutyric acid, propionic acid, and pantothenate; lower the levels of PC [18:0/18:1(9Z)], arachidonic acid, and docosahexaenoic acid.

Discussion

Thus, the results suggested that the PLP may perform the therapeutic activity via alleviating intestinal inflammation and regulating gut microbiota, avoiding further dysbiosis to restore the metabolism of gut microbiota, and finally promoting the recovery of diarrhea. The change further mitigated intestinal inflammation and oxidative damage in diarrheal calves. This indicated that PLP might be a promising treatment to attenuate diarrhea in neonatal calves.

A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples

Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.

To Save Pangolins: A Nutritional Perspective

Pangolins are one of the world's most trafficked mammals. Since pangolins are highly adapted to ants and termites, they are important for controlling forest termite infestations. In addition to their ecological value, pangolins have economic and medicinal value. Currently, poaching and habitat destruction have radically reduced the number of pangolins, and Manis pentadactyla, Manis javanica, and Manis culionensis are now considered the most threatened pangolin species. In addition to the control of hunting and illegal trade, ex situ breeding is also a useful conservation method. However, many technical obstacles still limit the success of ex situ pangolin breeding. The special feeding traits of pangolins require a diet that meets nutritional and ethological needs. Based on the existing literature and practical experience, this review aims to compare the natural diet and successful diet in the human care of pangolins, to outline the key factors of successful ex situ maintenance from a dietary perspective, and the strategies to improve their conservation success in animal care centers and in the wild. The type of food used in successful pangolin protection agencies is quite variable in nutritional composition. In the diet of pangolins in the wild, the nutrient profile of different species of termites and ants and even the same species of termites and ants but different types (queens, soldiers, etc.) also displays differences. The crude protein content of some ants is higher than that of other foods, such as eggs, milk, and common cat food. The mineral and vitamin concentrations of ants also exceed many common food items, such as oil, meat, and eggs. However, not much is known about the bioavailability of minerals from ants and termites. Based on comparisons between foods, it is clear that the main difference between diets in the wild and in human care of pangolins is that the latter contains fewer insects and vitamins, such as vitamin E, vitamin A, and vitamin B2, and more carbohydrates and non-protein substances than the former. Although many successful dietary formulae have been developed, the pangolin's nutritional needs are still less well studied. A diet with the nutrient concentrations observed in the wild may add to successful ex situ conservation.

Pre-transplant Ratio of Firmicutes/Bacteroidetes of Gut Microbiota as a Potential Biomarker of Allograft Rejection in Renal Transplant Recipients

The advent of technologies has made allogenic transplantation a potential curative therapy for end-stage renal diseases, but the episodes of rejection still remain as one of the challenges in the post-transplant scenario. In the recent years, several human and animal studies have elucidated that gut microbial dysbiosis is closely linked with allogenic transplantation and post-transplant complications. But most of the studies focused on the use of high through-put sequencing technologies to analyze gut microbiota despite of its high cost, analysis and time constraints. Hence, in this work we aimed to study the impact of the two dominant gut phyla Firmicutes and Bacteroidetes on 38 renal transplant recipients, before and after transplantation and to find its association with allograft rejection. Significant changes (p<0.01) were observed in the relative abundances of the phyla Firmicutes and Bacteroidetes at pre- and post-transplant period. We have also found that the recipients who had an increase in Firmicutes/Bacteroidetes (F/B) ratio before transplant were highly prone to rejection in the first-year post-transplant. The Receiver Operating Characteristic (ROC) curve analysis has shown that the ratio of F/B were able to discriminate between rejection and non-rejection cases with an Area under the ROC Curve (AUC) of 0.91. Additionally, we observed that the ratio of F/B have reduced during the time of rejection postulating that gut microbial dysbiosis has more association with rejection. Thus, the assessment of F/B ratio using qPCR would be of a more practical approach for diagnosis and monitoring of graft function in a cost-effective and timely manner.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

Analysis of Gut Microbiota and Metabolites in Diannan Small Ear Sows at Diestrus and Metestrus

The physiological state of the host affects the gut microbes. The estrus cycle is critical to the reproductive cycle of sows. However, the association between gut microbes and animal estrus is poorly understood. Here, high-throughput 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS) non-targeted metabolome technology were used to study the estrous cycles in Diannan small ear pigs. Significantly different gut microbiota and metabolites of sows at estrous and diestrus were screened out and the correlation was analyzed. We found that the intestinal microbial composition and microbial metabolism of Diannan small ear sows were significantly different at diestrus and metestrus. The abundances of Spirochaetes, Spirochaetia, Spirochaetales, Spirochaetaceae, Deltaproteobacteria, unidentified_Alphaproteobacteria, Ruminococcus_sp_YE281, and Treponema_berlinense in intestinal microorganisms of Diannan small ear sows at metestrus are significantly higher than that at diestrus. Propionic acid, benzyl butyrate, sucrose, piperidine, and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) were significantly enriched at metestrus compared with diestrus, which were involved in the energy metabolism-related pathways and activated protein kinase (AMPK) signaling pathway. At diestrus and metestrus, differential microbiota of unidentified_Alphaproteobacteria, Intestinimonas, Peptococcus, Terrisporobacter, and differential metabolites of piperidine, propionic acid, and benzyl butyrate, sucrose, 4-methyl catechol, and AICAR exist a certain degree of correlation. Therefore, unidentified_Alphaproteobacteria, Ruminococcus_sp_YE281, and Treponema_berlinense may have a potential role at metestrus of the Diannan small ear sows. AICAR may be apotential marker of estrus Diannan small ear sows feces, but further studies about the specific mechanism are needed. These findings provide a new perspective for sows production management and improving sows reproductive performance.

Gut microbiota reveals the environmental adaption in gastro-intestinal tract of wild boar in karst region of Southwest China

Background

Gut microbes has become one of the research hotspots in animal ecology, playing an important role in monitoring dietary adaptation and health status of host. However, there are few studies on the gut microbiota in the stomach, smallintestine (ileum), and large intestine (cecum, colon, and rectum) of wild boar.

Results

Alpha diversity and Beta diversity showed there were significant differences in the abundance and distribution of microbes in gastrointestinal tract of wild boar. Firmicutes and Bacteroidetes were the most dominant phyla in stomach, cecum, colon and rectum of wild boar, while Proteobacteria and Firmicutes were the most dominant in ileum. At genus level, there were different leading genera in stomach (Prevotella and Lactobacillus), small intestine (Escherichia-Shigella and Lactobacillus), and large intestine (Ruminococcaceae_UCG-005, Christensenellaceae_R-7_group, and Escherichia-Shigella). PICRUSt function predictive analysis suggested that there were significant differences in microbial metabolic pathways among five locations of wild boar.

Conclusions

This study comprehensively revealed the differences in composition of microbial community in gastrointestinal trac of wild boar. Future work links microbes with the metabolites to accurately reveal the health of wild boar.

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

Background

Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq.

Results

We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones.

Conclusions

Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00141-0.

Molecular detection and genotyping of Enterocytozoon bieneusi in captive foxes in Xinxiang, Central China and its impact on gut bacterial communities

Enterocytozoon bieneusi is a common gastrointestinal parasite that has a broad range of hosts, including birds, mammals, and even humans. The changes of gut bacterial communities have been demonstrated during the course of E. bieneusi. This study aimed to examine the infection status, and assess the zoonotic potential and influence of E. bieneusi on gut bacterial communities of captive foxes in Xinxiang, central China. Fecal samples were collected from 216 captive foxes, and amplification of the internal transcribed spacer (ITS) gene of each sample was performed by nested polymerase chain reaction. E. bieneusi was detected in 48 (22.2%) samples, and five previously reported genotypes CHN-F1 (n = 25), D (n = 18), BEB6 (n = 3), NCF2 (n = 1), and CHN-DC1 (n = 1) were identified, with CHN-F1 being the dominant genotype (25/48, 52.1%). Phylogenetic analysis further revealed that CHN-F1, D, NCF2, and CHN-DC1 genotypes belonged to the zoonotic group 1 of E. bieneusi, whereas BEB6 belonged to group 2. Moreover, sequencing and bioinformatics analysis of the V3-V4 region of 16S rRNA gene in five E. bieneusi-positive and five negative samples showed that gut microbial diversity was higher in the infected animals. In both groups, Firmicutes and Bacteroidetes were the two most abundant phyla, but the Firmicutes/Bacteroidetes ratio was lower in E. bieneusi-positive foxes (7.9:1) as compared with E. bieneusi-negative foxes (5:1). More importantly, at the phylum level, "beneficial bacteria" such as Firmicutes (1.6%) and Bacteroides (5.8%) increased, whereas "opportunistic pathogens" such as Fusobacteria (8.2%) decreased. Similarly, at the genus level, the pathogenic Clostridiaceae_Clostridium (10.0%) decreased, whereas the "beneficial bacteria" Lactococcus (6.6%) increased. These interesting phenomena warrant further investigation.

The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves

The genomic signature of dog domestication reveals adaptation to a starch-rich diet compared with their ancestor wolves. Diet is a key element to shape gut microbial populations in a direct way as well as through coevolution with the host. We investigated the dynamics in the gut microbiota of dogs when shifting from a starch-rich, processed kibble diet to a nature-like raw meat diet, using wolves as a wild reference. Six healthy wolves from a local zoo and six healthy American Staffordshire Terriers were included. Dogs were fed the same commercial kibble diet for at least 3 months before sampling at day 0 (DC), and then switched to a raw meat diet (the same diet as the wolves) for 28 days. Samples from the dogs were collected at day 1 (DR1), week 1 (DR7), 2 (DR14), 3 (DR21), and 4 (DR28). The data showed that the microbial population of dogs switched from kibble diet to raw diet shifts the gut microbiota closer to that of wolves, yet still showing distinct differences. At phylum level, raw meat consumption increased the relative abundance of Fusobacteria and Bacteroidetes at DR1, DR7, DR14, and DR21 (q < 0.05) compared with DC, whereas no differences in these two phyla were observed between DC and DR28. At genus level, Faecalibacterium, Catenibacterium, Allisonella, and Megamonas were significantly lower in dogs consuming the raw diet from the first week onward and in wolves compared with dogs on the kibble diet. Linear discriminant analysis effect size (LEfSe) showed a higher abundance of Stenotrophomonas, Faecalibacterium, Megamonas, and Lactobacillus in dogs fed kibble diet compared with dogs fed raw diet for 28 days and wolves. In addition, wolves had greater unidentified Lachnospiraceae compared with dogs irrespective of the diets. These results suggested that carbohydrate-fermenting bacteria give way to protein fermenters when the diet is shifted from kibble to raw diet. In conclusion, some microbial phyla, families, and genera in dogs showed only temporary change upon dietary shift, whereas some microbial groups moved toward the microbial profile of wolves. These findings open the discussion on the extent of coevolution of the core microbiota of dogs throughout domestication.

Habitat environmental factors influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

The short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5^TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

Dose-Dependent Effects of Dietary Xylooligosaccharides Supplementation on Microbiota, Fermentation and Metabolism in Healthy Adult Cats

In order to investigate the effect and appropriate dose of prebiotics, this study evaluated the effect of two levels of xylooligosaccharides (XOS) in cats. Twenty-four healthy adult cats were divided into three groups: no-XOS control diet with 1% cellulose; low XOS supplementation (LXOS) with 0.04% XOS and 0.96% cellulose; and high XOS supplementation (HXOS) with 0.40% XOS and 0.60% cellulose. Both XOS groups increased blood 3-hydroxybutyryl carnitine levels and decreased hexadecanedioyl carnitine levels. Both XOS treatments displayed an increased bacterial abundance of Blautia, Clostridium XI, and Collinsella and a decreased abundance of Megasphaera and Bifidobacterium. LXOS groups increased fecal pH and bacterial abundance of Streptococcus and Lactobacillus, decreased blood glutaryl carnitine concentration, and Catenibacterium abundance. HXOS group showed a more distinct microbiome profile and higher species richness, and an increased bacterial abundance of Subdoligranulum, Ruminococcaceae genus (unassigned genus), Erysipelotrichaceae genus, and Lachnospiraceae. Correlations between bacterial abundances and blood and fecal parameters were also observed. In conclusion, XOS could benefit feline gut health by altering microbiota; its effects dependant on the dose. The higher-dose XOS increased bacterial populations that possibly promoted intestinal fermentation, while the lower dose altered populations of carbohydrate-metabolic microbiota and possibly modulated host metabolism. Low-dose prebiotics may become a trend in future studies.

Integrating Gut Bacterial Diversity and Captive Husbandry to Optimize Vulture Conservation

Endangered species recovery plans often include captive breeding and reintroduction, but success remains rare. Critical for effective recovery is an assessment of captivity-induced changes in adaptive traits of reintroduction candidates. The gut microbiota is one such trait and is particularly important for scavengers exposed to carcass microbiomes. We investigated husbandry-associated differences in the gut microbiota of two Old World vulture species using 16S RNA gene amplicon sequencing. Increased abundance of Actinobacteria occurred when vultures were fed quail but not rat or chicken. Conversely, diet preparation (sanitization) had no effect, although bacterial diversity differed significantly between vulture species, likely reflective of evolved feeding ecologies. Whilst the relative lack of influence of a sanitized diet is encouraging, changes in bacterial abundance associated with the type of prey occurred, representing a dietary influence on host–microbiome condition warranting consideration in ex situ species recovery plans. Incorporation of microbiome research in endangered species management, therefore, provides an opportunity to refine conservation practice.

Regulation and analysis of the diversity of intestinal microbiota in SD rats by Danggui Buxue Tang (DBT) fermented with Bacillus subtilis

Purpose

To investigate the effect of Danggui Buxue Tang (DBT) on intestinal microbiota diversity after fermentation by Bacillus subtilis.

Methods

B. subtilis was used to ferment DBT. Sprague Dawley (SD) rats were randomly divided into the following four groups with six rats in each group: the control group, DBT nonfermentation group, B. subtilis group, and DBT fermentation group. Rats were fed continuously for 14 days. The 16S rRNA of faecal samples was analysed by high-throughput Illumina sequencing.

Results

In total, 3483 operational taxonomical units (OTUs) were identified in this study, and 1236 OTUs were shared among all samples. Moreover, the most abundant phyla identified in this study were Bacteroidetes (29.65–38.19%) and Firmicutes (48.30–67.04%). The F/B ratios of the DBT nonfermentation group (1.07%) and the DBT fermentation group (1.78%) were slightly lower than those of the control group (2.29%). Lactobacillus was most upregulated in the DBT fermentation group (38.4%), followed by the DBT nonfermentation group (18.97%), control group (14.61%), and probiotics group (8.39%). Moreover, the pathogenic bacteria Alistipes and Parabacteroides were found to be downregulated in the DBT fermentation group (the percentages of Alistipes and Parabacteroides were as follows: control group, 8.09% and 0.16%; DBT nonfermentation group, 4.31% and 0.37%; DBT fermentation group, 1.96 and 0.09%; and probiotics group, 6.25% and 0.12%, respectively).

Conclusion

This study is the first to research systematically the effects of DBT on the diversity of rat intestinal microbiota before and after fermentation. The structural characteristics of complex bacterial community in each group were clearly analysed, and DBT significantly increases probiotics and inhibits pathogenic bacterial growth in the intestinal tract of rats after fermentation, which plays a significant role in maintaining the balance of the intestinal microbiota of the rats. This research provides new insights into the development and utilization of traditional Chinese medicine.

The fecal microbiota of wild and captive raptors

BACKGROUND

The microorganisms populating the gastro-intestinal tract of vertebrates, collectively known as "microbiota", play an essential role in digestion and are important in regulating the immune response. Whereas the intestinal microbiota in humans and model organisms has been studied for many years, much less is known about the microbiota populating the intestinal tract of wild animals.

RESULTS

The relatively large number of raptors admitted to the Tufts Wildlife Clinic on the Cummings School of Veterinary Medicine at Tufts University campus provided a unique opportunity to investigate the bacterial microbiota in these birds. Opportunistic collection of fecal samples from raptors of 7 different species in the orders Strigiformes, Accipitriformes, and Falconiformes with different medical histories generated a collection of 46 microbiota samples. Based on 16S amplicon sequencing of fecal DNA, large β-diversity values were observed. Many comparisons exceeded weighted UniFrac distances of 0.9. Microbiota diversity did not segregate with the taxonomy of the host; no significant difference between microbiota from Strigiformes and from Accipitriformes/Falconiformes were observed. In contrast, in a sample of 22 birds admitted for rehabilitation, a significant effect of captivity was found. The change in microbiota profile was driven by an expansion of the proportion of Actinobacteria. Based on a small number of raptors treated with anti-microbials, no significant effect of these treatments on microbiota α-diversity was observed.

CONCLUSIONS

The concept of "meta-organism conservation", i.e., conservation efforts focused on the host and its intestinal microbiome has recently been proposed. The observed effect of captivity on the fecal microbiota is relevant to understanding the response of wildlife to captivity and optimizing wildlife rehabilitation and conservation efforts.

Gut microbiota of red swamp crayfish Procambarus clarkii in integrated crayfish-rice cultivation model

Increasing evidences suggest that intestinal microbiota balance closely correlated with host’s health status could affected by external environment. Integrated crayfish-rice cultivation model is a highly efficient artificial ecosystem widely practiced in subtropical China. Less information is available to estimate the influence response to the micro-ecology of crayfish intestine and so as to influence the biological processes. Thus, 16S rRNA high-throughput sequencing approach was employed to investigate the composition diversity and functions of bacterial community in the intestines of Procambarus clarkii farmed within this model. Results exhibited the highly diversity of microflora with dominant phyla Actinobacteria, Proteobacteria, Tenericutes, Firmicutes and Bacteroidetes. The genera of Candidatus Bacilloplasma and Ornithinibacter were presented as predominant population much exceeds in richness comparing to that of other genus. Despite the highly diversity in the bacterial community, the predicted functions indicated relative consistent in biological processing pathway. Collectively, significant richness of genes was observed involved in amino acid and carbohydrate metabolism and membrane transport processing. This study would contribute to the understanding of the impact of growth conditions on host–microbiota relation especially in aquatic animals.

Comparative analysis of the gut microbiota of the blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides)

The goal of this study is to compare the gut microbiota of domestic blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides) to provide better understanding of their intestinal gut microbiota. We analyzed the structure of fecal microbes in 40 blue foxes and 40 raccoon dogs that were raised under same conditions, using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. In total, 295,146 sequence reads were obtained. The average number of operational taxonomical units in the two group samples was 194 to 286. Firmicutes (blue fox 73.40%, raccoon dog 46.90%) and Bacteroidetes (blue fox 21.92%, raccoon dog 44.25%) were the most abundant phyla in the gut of blue fox and raccoon dog. At the genus level, Prevotella (blue fox 16.89%, raccoon dog 36.22%), Blautia (blue fox 9.02%, raccoon dog 13.72%), and Peptostreptococcaeae_incertae_sedi (blue fox 22.41%, raccoon dog 2.84%) were commonly presented in the gut of two kinds of animal. Principal coordinates analysis showed that the microbial communities were different between blue fox and raccoon dog. The Firmicutes-to-Bacteroidetes ratio was higher in blue foxes (3:1) than in raccoon dogs (1:1). Moreover, Peptostreptococcaeae_incertae_sedi and Prevotella, were more abundant in the gut of blue fox, whereas the abundance of Prevotella and Blautia were higher in the gut of raccoon dog. In conclusion, the present study revealed the difference of the gut microbial composition between blue fox and raccoon dog under the same diet conditions.

Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.

Comparative molecular analysis of fecal microbiota of bobcats (Lynx rufus) and domestic cats (Felis catus)

The goal of this study was to explore and describe fecal microbiota of captive and wild bobcats (Lynx rufus) and compare the results to those of domestic cats (Felis catus). Fecal samples from 27 bobcats (8 wild, 19 zoo-kept) were used for novel bacterial deoxyribonucleic acid (DNA) identification using next-generation sequencing of the V4 region of the bacterial 16S ribosomal ribonucleic acid (rRNA) gene, analyzed by Illumina sequencing, and then compared to data obtained from a colony of 10 domestic cats. In this study, the microbiota of both species was dominated by Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. When compared, fecal samples from bobcats harbored more Proteobacteria and Actinobacteria than fecal samples from domestic cats. There was a remarkable inter-bobcat variation in the relative abundances of the main bacterial genera. There were no significant differences, however, between the main phyla of the microbiota of the wild and domestic bobcats. Proteobacteria in wild bobcats (P = 0.079) and Firmicutes in zoo-kept bobcats (P = 0.079) approached significance. There were no differences in predominant genera between wild and captive bobcats. The results of this study showed that there are notable differences in fecal bacterial communities between domestic cats and both captive and wild bobcats. The lack of significant differences in bacterial communities between wild and zoo-kept bobcats suggests that the varied diet provided for these felids can result in a fecal microbiota resembling that generated by a wild diet.

Effects of Transgenic Bt Rice Containing the Cry1Ab Protein on the Gastrointestinal Health of Highly Inbred Wuzhishan Pigs after Two Generations of Feeding

To assess the safety of transgenic Bt rice, we evaluated the chronic effects of Bt rice carrying the Cry1Ab protein (1.64 mg/kg) on the gut microbiota and histopathology in highly inbred Wuzhishan pigs (WZSP) in a two-generation feeding study. The WZSP of the f0 ( n = 26) and f1 ( n = 27) generations were divided into GM and Non-GM groups and fed for 360 and 420 days with Bt and isogenic parent-line rice, respectively. The high-throughput 16S rRNA gene sequencing results revealed that the relative abundance of the family Enterobacteriaceae and genus Escherichia were significantly different between f1F and f1Z. The level of the genera CF231 and SMB53 in the f0Z group was higher than that in the f0F group. In addition, no abnormal histopathology changes in the main gastrointestinal tissues were found after feeding with Bt rice. In conclusion, Bt rice consumption has no adverse effects on the gut microbiota or organ function of WZSP.

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest

Research on the gut microbiota of free-ranging mammals is offering new insights into dietary ecology. However, for free-ranging primates, little information is available for how microbiomes are influenced by ecological variation through time. Primates inhabiting seasonal tropical dry forests undergo seasonally specific decreases in food abundance and water availability, which have been linked to adverse health effects. Throughout the course of a seasonal transition in 2014, we collected fecal samples from three social groups of free-ranging white-faced capuchin monkeys (Cebus capucinus imitator) in Sector Santa Rosa, Área de Conservación Guanacaste, Costa Rica. 16S rRNA sequencing data reveal that unlike other primates, the white-faced capuchin monkey gut is dominated by Bifidobacterium and Streptococcus. Linear mixed effects models indicate that abundances of these genera are associated with fluctuating availability and consumption of fruit and arthropods, whereas beta diversity clusters by rainfall season. Whole shotgun metagenomics revealed that the capuchin gut is dominated by carbohydrate-binding modules associated with digestion of plant polysaccharides and chitin, matching seasonal dietary patterns. We conclude that rainfall and diet are associated with the diversity, composition, and function of the capuchin gut microbiome. Additionally, microbial fluctuations are likely contributing to nutrient uptake and the health of wild primate populations.

Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas

To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus

To understand the effect of woody forages on golden pompano (Trachinotus ovatus) intestinal bacteria diversity and exploit new aquafeed ingredients, the diets of Moringa oleifera Lam (MOL), Broussonetia papyrifera (BP), Neolamarckia cadamba (NC) and Folium mori (FM) formulated with 70% of reference (Ref) diet and 30% of the four woody plants leaves were fed to golden pompano with initial body weight of 34.4 ± 0.5 g for 56 days, respectively. Bacteria diversity of golden pompano intestine and tank water (W) samples were analyzed using high-throughput illumina sequencing and the result indicated that the dominate phyla of golden pompano intestine were Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. Proteobacteria in BP was significantly higher than those in NC (P < 0.05). Firmicutes in NC were significantly higher than those in BP and FM (P < 0.05). At genera level, Lactobacillus in NC was significantly higher than those in BP, MOL and FM groups (P < 0.05). The PCoA and heat map analyses showed that the intestinal bacteria community of golden pompano fed with woody forages and Ref diet presented higher similarity and the bacteria community of golden pompano intestine were clearly distinguished from those of W. Phylogenetic investigation of communities by reconstruction of unobserved states showed that the intestinal bacteria dominant metabolism pathways of golden pompano fed with woody forages and Ref diet were biosynthesis of amino acids and carbon metabolism. Overall, the present study first successfully characterized the intestinal bacteria diversity of golden pompano.

Are carnivore digestive separation mechanisms revealed on structure-rich diets?: Faecal inconsistency in dogs (Canis familiaris) fed day old chicks

Pronounced variations in faecal consistency have been described anecdotally for some carnivore species fed a structure-rich diet. Typically two faecal consistencies are distinguished, namely hard and firm versus liquid and viscous faeces. It is possible that a separation mechanism is operating in the carnivore digestive tract, as in many herbivore species. Six beagle dogs were fed two experimental diets in a cross-over design of 7 days. Test diets consisted of chunked day old chicks differing only in particle size (fine = 7.8 mm vs coarse = 13 mm) in order to vary dietary structure. Digestive retention time was measured using titanium oxide (TiO2) as marker. The total faecal output was scored for consistency and faecal fermentation profiles were evaluated through faecal short-chain fatty acid (SCFA) and ammonia (NH3) analyses. A total of 181 faecal samples were collected. Dietary particle size did not affect faecal consistency, fermentative end products nor mean retention time (MRT). However, a faecal consistency dichotomy was observed with firm faeces (score 2-2.5) and soft faeces (score 4-4.5) being the most frequently occurring consistencies in an almost alternating pattern in every single dog. Firm and soft faeces differed distinctively in fermentative profiles. Although the structure difference between diets did not affect the faecal dichotomy, feeding whole prey provoked the occurrence of the latter which raises suspicion of a digestive separation mechanism in the canine digestive tract. Further faecal characterisation is however required in order to unravel the underlying mechanism.

Gut microbiomes of free-ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens

Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free-ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free-ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease-associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management.

Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene

Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host's health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63-38.97 %), Firmicutes (20.97-44.01 %), Proteobacteria (9.33-17.60 %), Fusobacteria (9.11-17.90 %), and Actinobacteria (1.22-2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.

Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs

Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus), this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05), and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%). This observation may reflect the temporary impact of perturbations such as the animal’s compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five animals under study that may typify the core phylogenetic microbiome of cheetahs.

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.