The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds

The impact of management on the fecal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program

Greater sage-grouse (Centrocercus urophasianus) are a critically endangered species in Canada with fewer than 140 individuals remaining on native habitats in southern Alberta and Saskatchewan. In 2014, the Wilder Institute/Calgary Zoo initiated North America's only zoo-based conservation breeding program for this species to bolster declining wild populations through conservation reintroductions. Within the managed population of sage-grouse, morbidity and mortality have primarily been associated with intestinal bacterial infections. As a preliminary study to assess the gastrointestinal health of this species in managed care, the fecal bacterial microbiome of adult and juvenile captive sage-grouse was characterized with 16S rRNA sequencing. The composition of the microbiome at the phylum level in greater sage-grouse is consistent with previous studies of the avian microbiome, with Bacillota as the most abundant phyla, and Actinomycetota, Bacteroidota and Pseudomonadota also being highly abundant. Antibiotic use and sex did not have a significant impact on the diversity or composition of the microbiome, but the management of juvenile sage-grouse did influence the development of the microbiome. Juveniles that were raised outdoors under maternal care developed a microbiome much more similar to adults when compared to chicks that were incubated and hand-raised. The local environment and parental care appear to be important factors influencing the diversity and composition of the gastrointestinal microbiome in this species.

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika

Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.

Change of termite hindgut metabolome and bacteria after captivity indicates the hindgut microbiota provides nutritional factors to the host

The gut-dwelling microbiota is an indispensable part of termites. It is influenced by a series of factors, such as diet and captivity. The objectives of this study were to study the metabolic functions of hindgut microbiota and to investigate the influence of captivity on the hindgut microbiota. The dampwood termite Hodotermopsis sjostedti was reared in the laboratory for 6 months. We conducted the metabolome analysis of the fat body from the freshly-collected workers (FBF), the hindgut fluid of the freshly-collected workers (HFF), and the hindgut fluid of laboratory-maintained workers. In addition, the 16S rRNA genes from the hindgut bacteria in the freshly-collected and laboratory-maintained workers were sequenced. According to our results, the concentrations of metabolites associated with amino acid biosynthesis, vitamin biosynthesis, fatty acid biosynthesis, and cofactor biosynthesis were higher in HFF compared with those in FBF, suggesting that the hindgut microbiota provides nutritional factors to the host. However, after captivity, the concentrations of metabolites in the hindgut associated with amino acid biosynthesis, nucleotide sugar metabolism, vitamin biosynthesis, and carbon metabolism decreased, while those associated with the steroid hormone biosynthesis and ovarian steroidogenesis increased. Meanwhile, the 16S amplicon study revealed that the abundance of certain bacteria changed after captivity, such as uncultured Termite Group 1 bacterium, Candidatus Symbiothrix dinenymphae, and unclassified Desulfovibrio. Our findings show that captivity influences the hindgut microbiota and shed light on the metabolic potential of the hindgut microbiota.

Surveys of eleven species of wild and zoo birds and feeding experiments in white-tailed eagles reveal differences in the composition of the avian gut microbiome based on dietary habits between and within species

The composition of the gut microbiome varies due to dietary habits. We investigated influences of diet on the composition of the gut microbiome using the feces of 11 avian species, which consumed grain-, fish- and meat-based diets. We analyzed gut microbiome diversity and composition by next-generation sequencing (NGS) of 16S ribosomal RNA. The grain-diet group had higher gut microbiome diversity than the meat- and fish-diet group. The ratio of Bacteroidetes and Firmicutes phyla was higher in the grain-diet group than in the meat- and fish-diet groups. The grain-diet group had a higher ratio of Veillonellaceae than the meat-diet group and a higher ratio of Eubacteriaceae than the fish-diet habit group. To clarify the influence of diet within the same species, white-tailed eagles (Haliaeetus albicilla, n=6) were divided into two groups, and given only deer meat or fish for approximately one month. The composition of the gut microbiome of individuals in both groups were analyzed by NGS. There were indications of fluctuation in the levels of some bacteria (Lactobacillus, Coriobacteriales, etc.) in each diet group. Moreover, one individual for each group which switched each diet in last week changed to each feature of composition of bacterial flora. The above results show that the composition of the gut microbiome differ depending on diet, even within the same species.

Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes (Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China

The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).

First detection of herpesvirus and hemosporidians in the endangered Pyrenean Capercaillie (Tetrao urogallus aquitanicus)

Pathogens affect wild bird populations worldwide, contributing to their decline. Considering the scarce health data regarding the endangered Pyrenean Capercaillie (Tetrao urogallus aquitanicus), we molecularly surveyed selected pathogens (Newcastle disease virus, Avian influenza virus, Chlamydia psittaci, avian pathogenic Escherichia coli, Campylobacter jejuni, and Salmonella spp.) in 30 Pyrenean Capercaillie feces collected in the field (Catalonia, northeastern Spain). Additionally, swab and tissue samples from eight wild Pyrenean Capercaillies of Catalonia and Andorra were molecularly tested for herpesvirus and hemosporidians (Plasmodium spp., Haemoproteus spp., and Leucocytozoon spp.). All fecal samples were negative for the pathogens tested. Nevertheless, we detected a novel herpesvirus in 50% (4/8) of the Pyrenean Capercaillies, and hemosporidian DNA in 62.5% (5/8) of the tissue samples (i.e., Haemoproteus sp. [4 of 8] and/or Leucocytozoon sp. [3 of 8]). To our knowledge, this is the first detection of herpesvirus and hemosporidians infections in Pyrenean Capercaillies. The putative novel herpesvirus belongs to the genus Iltovirus. The presence of hemosporidian parasites in this mountain bird species is of concern, and could be related to the marked increase in the average temperature in the Pyrenees as a consequence of climate change. Our findings are fundamental to improve the conservation plans for the endangered Pyrenean Capercaillie population.

Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities

Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.

The microbiome of African penguins (Spheniscus demersus) under managed care resembles that of wild marine mammals and birds

Animals under managed care in zoos and aquariums are ideal surrogate study subjects for endangered species that are difficult to obtain in the wild. We compared the fecal and oral microbiomes of healthy, managed African penguins (Spheniscus demersus) to those of other domestic and wild vertebrate hosts to determine how host identity, diet, and environment shape the penguin microbiome. The African penguin oral microbiome was more similar to that of piscivorous marine mammals, suggesting that diet and a marine environment together play a strong role in shaping the oral microbiome. Conversely, the penguin cloaca/fecal microbiome was more similar to that of other birds, suggesting that host phylogeny plays a significant role in shaping the gut microbiome. Although the penguins were born under managed care, they had a gut microbiome more similar to that of wild bird species compared to domesticated (factory-farmed) birds, suggesting that the managed care environment and diet resemble those experienced by wild birds. Finally, the microbiome composition at external body sites was broadly similar to that of the habitat, suggesting sharing of microbes between animals and their environment. Future studies should link these results to microbial functional capacity and host health, which will help inform conservation efforts.

Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella, were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella. Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome

The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.

Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center

The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.

Mortality Causes in Captive Cantabrian capercaillie (Tetrao urogallus cantabricus) in Spain

The Cantabrian capercaillie (Tetrao urogallus cantabricus) is one of the most severely threatened subspecies of capercaillie. Its current population range is restricted to a small area of the Cantabrian Mountains (northwestern Spain), with only around 200 individuals remaining. As part of the national strategy for the conservation of the subspecies, the Cantabrian capercaillie Captive Breeding Center of Sobrescobio opened in 2009. Here, we use the information provided by the necropsies performed in this facility on 29 individuals (11 males, 13 females and 5 undetermined; 16 chicks and 13 adults) in order to describe the main mortality causes of captive-bred Cantabrian capercaillies. After necropsy, tissue samples were taken for evaluation using standard methods in histology and microbiology. The majority of the captive animals (18/29, 62.07%) died due to infectious diseases, mainly due to Escherichia coli, Clostridium perfringens, or Aspergillus fumigatus infection. The remaining 11 animals died due to stress-related processes (i.e., rupture of the heart apex and cardiomyopathy or neurogenic shock) (8/29, 27.59%), duodenal obstruction and coelomitis (1/29, 3.45%), perforation of the proventriculus and heart with a briar branch (1/29, 3.45%) or euthanasia due to a valgus leg deformity that prevented proper animal welfare (1/29, 3.45%). Young animals (i.e., younger than 2 months) died mainly due to infectious diseases (14/16, 87.5%), while stress-related causes were responsible for most adult deaths (7/13, 53.85%). We additionally report that two free-ranging adult males died due to exertional myopathy. This study provides relevant information for reducing mortality in captive capercaillies and improving both living conditions in captivity and the adaptation of these animals to the wild.

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community

The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.

Discrete patterns of microbiome variability across timescales in a wild rodent population

Mammalian gastrointestinal microbiomes are highly variable, both within individuals and across populations, with changes linked to time and ageing being widely reported. Discerning patterns of change in wild mammal populations can therefore prove challenging. We used high-throughput community sequencing methods to characterise the microbiome of wild field voles (Microtus agrestis) from faecal samples collected across 12 live-trapping field sessions, and then at cull. Changes in α- and β-diversity were modelled over three timescales. Short-term differences (following 1–2 days captivity) were analysed between capture and cull, to ascertain the degree to which the microbiome can change following a rapid change in environment. Medium-term changes were measured between successive trapping sessions (12–16 days apart), and long-term changes between the first and final capture of an individual (from 24 to 129 days). The short period between capture and cull was characterised by a marked loss of species richness, while over medium and long-term in the field, richness slightly increased. Changes across both short and long timescales indicated shifts from a Firmicutes-dominant to a Bacteroidetes-dominant microbiome. Dramatic changes following captivity indicate that changes in microbiome diversity can be rapid, following a change of environment (food sources, temperature, lighting etc.). Medium- and long-term patterns of change indicate an accrual of gut bacteria associated with ageing, with these new bacteria being predominately represented by Bacteroidetes. While the patterns of change observed are unlikely to be universal to wild mammal populations, the potential for analogous shifts across timescales should be considered whenever studying wild animal microbiomes. This is especially true if studies involve animal captivity, as there are potential ramifications both for animal health, and the validity of the data itself as a reflection of a ‘natural’ state of an animal.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae)

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia (Leiothrix argentauris) living in mining area

The complex gut bacterial communities have a major impact on organismal health. However, knowledge of the effects of habitat change on the gut microbiota of wild birds is limited. In this study, we characterized the gut microbiota of two different subspecies of the Silver-eared Mesia (Leiothrix argentauris), the native subspecies (L. a. rubrogularis) and immigrant subspecies (L. a. vernayi), using 16S rRNA gene high-throughput sequencing. These two subspecies live in a trace metal-contaminated area, and L. a. vernayi was trafficked. They are an excellent system for studying how the gut microbiome of wild animal changes when they move to new habitats. We hypothesized that the immigrant subspecies would develop the same adaptations as the native subspecies in response to habitat changes. The results showed that there were no significant differences in the composition, diversity, or functional metabolism of gut microbiota between native and immigrant subspecies under the combined action of similar influencing factors (the p values of all analyses of variance >0.05). In addition, the composition and functional metabolism of gut microbiota in two subspecies showed adaptation against trace metal damage. Linear discriminant analysis effect size (LEfSe) analysis revealed that Massilia in the intestinal microbiota of immigrant subspecies was significantly higher than that of native subspecies, suggesting that immigrant subspecies suffered habitat change. Finally, we found that these two subspecies living in the mining area had an extremely high proportion of pathogenic bacteria in their gut microbiota (about 90%), much higher than in other species (about 50%) living in wild environment. Our results revealed the adaptation of intestinal microbiota of immigrant Silver-eared Mesias under heavy metals stress, which would provide guidance for biodiversity conservation and pollution management in mining area.

Effects of short-term experimental manipulation of captive social environment on uropygial gland microbiome and preen oil volatile composition

Introduction

Avian preen oil, secreted by the uropygial gland, is an important source of volatile compounds that convey information about the sender’s identity and quality, making preen oil useful for the recognition and assessment of potential mates and rivals. Although intrinsic factors such as hormone levels, genetic background, and diet can affect preen oil volatile compound composition, many of these compounds are not the products of the animal’s own metabolic processes, but rather those of odor-producing symbiotic microbes. Social behavior affects the composition of uropygial microbial communities, as physical contact results in microbe sharing. We experimentally manipulated social interactions in captive dark-eyed juncos (Junco hyemalis) to assess the relative influence of social interactions, subspecies, and sex on uropygial gland microbial composition and the resulting preen oil odor profiles.

Methods

We captured 24 birds at Mountain Lake Biological Station in Virginia, USA, including birds from two seasonally sympatric subspecies – one resident, one migratory. We housed them in an outdoor aviary in three phases of social configurations: first in same-sex, same-subspecies flocks, then in male-female pairs, and finally in the original flocks. Using samples taken every four days of the experiment, we characterized their uropygial gland microbiome through 16S rRNA gene sequencing and their preen oil volatile compounds via GC-MS.

Results

We predicted that if social environment was the primary driver of uropygial gland microbiome composition, and if microbiome composition in turn affected preen oil volatile profiles, then birds housed together would become more similar over time. Our results did not support this hypothesis, instead showing that sex and subspecies were stronger predictors of microbiome composition. We observed changes in volatile compounds after the birds had been housed in pairs, which disappeared after they were moved back into flocks, suggesting that hormonal changes related to breeding condition were the most important factor in these patterns.

Discussion

Although early life social environment of nestlings and long-term social relationships have been shown to be important in shaping uropygial gland microbial communities, our study suggests that shorter-term changes in social environment do not have a strong effect on uropygial microbiomes and the resulting preen oil volatile compounds.

Comparative analysis of intestinal flora between rare wild red-crowned crane and white-naped crane

INTRODUCTION

Animal intestines are extremely rich in microbial ecosystems. Numerous studies in different fields, such as epidemiology and histology, have revealed that gut microorganisms considerably mediate the survival and reproduction of animals. However, gut microbiology studies of homogeneously distributed wild cranes are still rare. This study aimed to understand the structural composition of the gut microbial community of wild cranes and elucidate the potential roles of the microorganisms.

METHODS

We used high-throughput sequencing to analyze the gut microbial community structure of wild cranes in the Zhalong Nature Reserve.

RESULTS

A total of 1,965,683 valid tags and 5248 OTUs were obtained from 32 fecal samples. Twenty-six bacteria phyla and 523 genera were annotated from the intestinal tract of the red-crowned crane. Twenty-five bacteria phyla and 625 genera were annotated from the intestine of the white-naped crane. Firmicutes, Proteobacteria, and Bacteroidetes are the dominant bacterial phyla in the intestinal tract of red-crowned cranes, while Catellicoccus, Lactobacillus, Neisseria, and Streptococcus were the dominant genera. The dominant bacterial phyla in the intestinal tract of white-naped cranes were Firmicutes, Proteobacteria, Bacteroidetes, Epsilonbacteraeota, Actinobacteria, and Fusobacteria. However, the dominant genera were Catellicoccus, Lactobacillus, Neisseria, Campylobacter, Streptococcus, Anaerobiospirillum, Romboutsia, Turicibacter, Haemophilus, and Lautropia. Firmicutes had significantly higher relative abundance in the intestine of the red-crowned than white-naped cranes (P < 0.05). However, the relative abundance of Actinobacteria and Bacteroidetes was significantly higher (P < 0.05) in the intestines of white-naped than red-crowned cranes. The diversity of the intestinal flora between the two crane species was significantly different (P < 0.05). Besides, the alpha diversity of the intestinal flora was higher for white-naped than red-crowned cranes. Eight of the 41 functional pathways differed in the gut of both crane species (P < 0.05).

DISCUSSION

Both species live in the same area and have similar feeding and behavioral characteristics. Therefore, host differences are possibly the main factors influencing the structural and functional differences in the composition of the gut microbial community. This study provides important reference data for constructing a crane gut microbial assessment system. The findings have implications for studying deeper relationships between crane gut microbes and genetics, nutrition, immunity, and disease.

Uropygial gland microbiota differ between free-living and captive songbirds

Symbiotic microbes can affect host behavior and fitness. Gut microbiota have received the most study, with less attention to other important microbial communities like those of scent-producing glands such as mammalian anal glands and the avian uropygial gland. However, mounting evidence suggests that microbes inhabiting scent-producing glands play an important role in animal behavior by contributing to variation in chemical signals. Free-living and captive conditions typically differ in social environment, food diversity and availability, disease exposure, and other factors-all of which can translate into differences in gut microbiota. However, whether extrinsic factors such as captivity alter microbial communities in scent glands remains an open question. We compared the uropygial gland microbiota of free-living and captive song sparrows (Melospiza melodia) and tested for an effect of dietary manipulations on the gland microbiota of captive birds. As predicted, the uropygial gland microbiota was significantly different between free-living and captive birds. Surprisingly, microbial diversity was higher in captive than free-living birds, and we found no effect of dietary treatments on captive bird microbiota. Identifying the specific factors responsible for microbial differences among groups and determining whether changes in symbiotic microbiota alter behavior and fitness are important next steps in this field.

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)

Background

Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals.

Objectives

In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor.

Results

The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species.

Conclusions

Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota

Highland birds evolve multiple adaptive abilities to cope with the harsh environments; however, how they adapt to the high-altitude habitats via the gut microbiota remains understudied. Here we integrated evidences from comparative analysis of gut microbiota to explore the adaptive mechanism of black-necked crane, a typical highland bird in the Qinghai-Tibet Plateau. Firstly, the gut microbiota diversity and function was compared among seven crane species (one high-altitude species and six low-altitude species), and then among three populations of contrasting altitudes for the black-necked crane. Microbiota community diversity in black-necked crane was significantly lower than its low-altitude relatives, but higher microbiota functional diversity was observed in black-necked crane, suggesting that unique bacteria are developed and acquired due to the selection pressure of high-altitude environments. The functional microbial genes differed significantly between the low- and high-altitude black-necked cranes, indicating that altitude significantly impacted microbial communities' composition and structure. Adaptive changes in microbiota diversity and function are observed in response to high-altitude environments. These findings provide us a new insight into the adaptation mechanism to the high-altitude environment for birds via the gut microbiota. KEY POINTS: • The diversity and function of gut microbiota differed significantly between the low- and high-altitude crane species. • Black-necked crane adapts to the high-altitude environment via specific gut microbiota. • Altitude significantly impacted microbial communities' composition and structure.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse

Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r² = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r² = 0.070, P = 0.001) or their interaction (t = 3.449; r² = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome (T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds (T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).

Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity

Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.

Chronic stress and captivity alter the cloacal microbiome of a wild songbird

There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the “gut-brain axis;” however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we used a chronic mild stress protocol to induce stress in wild-caught house sparrows (Passer domesticus), and compared microbial communities among stressed animals, those recovering from stress, captive controls (unstressed), and a group not brought into captivity. We assessed changes in microbial communities and abundance of shed microbes by culturing cloacal samples on multiple media to select for aerobic and anaerobic bacteria and fungi. We complemented this with cultivation-independent 16S and ITS rRNA gene amplification and sequencing, pairing these results with host physiological and immune metrics, including body mass change, relative spleen mass, and plasma corticosterone concentrations. We found significant effects of stress and captivity on the house sparrow microbiomes, with stress leading to an increased relative abundance of endotoxin-producing bacteria— a possible mechanism for the hyperinflammatory response observed in captive avians. While we found evidence that the microbiome community partially recovers after stress cessation, animals may lose key taxa, and the abundance of endotoxin-producing bacteria persists. Our results suggest an overall link between chronic stress, host immune system, and the microbiome, with the loss of potentially beneficial taxa (e.g., lactic acid bacteria), and an increase in endotoxin-producing bacteria due to stress and captivity. Ultimately, consideration of the host's microbiome may be useful when evaluating the impact of stressors on individual and population health.

Effects of floor- and net-rearing systems on intestinal growth and microbial diversity in the ceca of ducks

BACKGROUND

Rearing systems can affect livestock production directly, but whether they have effects on intestinal growth states and ceca microorganisms in ducks is largely unclear. The current study used Nonghua ducks to estimate the effects of rearing systems on the intestines by evaluating differences in intestinal growth indices and cecal microorganisms between ducks in the floor-rearing system (FRS) and net-rearing system (NRS).

RESULTS

The values of relative weight (RW), relative length (RL) and RW/RL of the duodenum, jejunum, ileum and ceca in the FRS were significantly higher than those in the NRS during weeks 4, 8 and 13 (p < 0.05). A total of 157 genera were identified from ducks under the two systems, and the dominant microorganisms in both treatments were Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria at the phylum level. The distribution of microorganisms in the ceca of the two treatments showed significant separation during the three time periods, and the value of the Simpson index in the FRS was significantly higher than that in the NRS at 13 weeks (p < 0.05). Five differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 4, seven differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 8, and four differential microorganisms and two differential metabolic pathways were found in the ceca at week 13.

CONCLUSIONS

The rearing system influences duck intestinal development and microorganisms. The FRS group had higher intestinal RL, RW and RW/RL and obviously separated ceca microorganisms compared to those of the NRS group. The differential metabolic pathways of cecal microorganisms decreased with increasing age, and the abundance of translation pathways was higher in the NRS group at week 13, while cofactor and vitamin metabolism were more abundant in the FRS group.

No guts about it: captivity, but not neophobia phenotype, influences the cloacal microbiome of house sparrows (Passer domesticus)

Behavioral traits such as anxiety and depression have been linked to diversity of the gut microbiome in humans, domesticated animals, and lab-bred model species, but the extent to which this link exists in wild animals, and thus its ecological relevance, is poorly understood. We examined the relationship between a behavioral trait (neophobia) and the cloacal microbiome in wild house sparrows (Passer domesticus,n = 22) to determine whether gut microbial diversity is related to personality in a wild animal. We swabbed the cloaca immediately upon capture, assessed neophobia phenotypes in the lab, and then swabbed the cloaca again after several weeks in captivity to additionally test whether the microbiome of different personality types is affected disparately by captivity, and characterized gut microbiomes using 16S rRNA gene amplicon sequencing. We did not detect differences in cloacal alpha or beta microbial diversity between neophobic and non-neophobic house sparrows, and diversity for both phenotypes was negatively impacted by captivity. Although our results suggest that the adult cloacal microbiome and neophobia are not strongly linked in wild sparrows, we did detect specific OTUs that appeared more frequently and at higher abundances in neophobic sparrows, suggesting that links between the gut microbiome and behavior may occur at the level of specific taxa. Further investigations of personality and the gut microbiome are needed in more wild species to reveal how the microbiome-gut-brain axis and behavior interact in an ecological context.

Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing

BACKGROUND

Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring.

RESULTS

Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas.

CONCLUSIONS

This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.

Possibilities and limits for using the gut microbiome to improve captive animal health

Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.

Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts

BACKGROUND

Changes in wild animal gut microbiotas may influence host health and fitness. While many studies have shown correlations between gut microbiota structure and external factors, few studies demonstrate causal links between environmental variables and microbiota shifts. Here, we use a fully factorial experiment to test the effects of elevated ambient temperature and natural nest parasitism by nest flies (Protocalliphora sialia) on the gut microbiotas of two species of wild birds, the eastern bluebird (Sialia sialis) and the tree swallow (Tachycineta bicolor).

RESULTS

We find that bacterial communities from the nestlings of each host species show idiosyncratic responses to both heat and parasitism, with gut microbiotas of eastern bluebirds more disrupted by heat and parasitism than those of tree swallows. Thus, we find that eastern bluebirds are unable to maintain stable associations with their gut bacteria in the face of both elevated temperature and parasitism. In contrast, tree swallow gut microbiotas are not significantly impacted by either heat or nest parasitism.

CONCLUSIONS

Our results suggest that excess heat (e.g., as a result of climate change) may destabilize natural host-parasite-microbiota systems, with the potential to affect host fitness and survival in the Anthropocene.

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)

Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.

The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

Abstract

Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health.

Key points

• Swainsonine improves the intestinal bacterial diversity of plateau pikas.

• Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas.

• Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11478-6.

Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach

Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R² = 0.13, p = 10^–4, Adonis R² = 0.11, p = 10^–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.

Polar bear-adapted Ursidibacter maritimus are remarkably conserved after generations in captivity

Most species in the bacterial family of Pasteurellaceae colonize one specific host species. Vertebrates of very different evolutionary descent including fish, turtles, marsupials, eutherians and birds are colonized by different members of Pasteurellaceae. This one-to-one microbial-host species partnership makes Pasteurellaceae species valuable candidates to study biodiversity, bacterial-host co-evolution and host adaptation, and their widespread distribution across vertebrates provide the possibility to collect a wide array of data, where wildlife species are essential. However, obtaining samples from wild animals comes with logistic, technical and ethical challenges, and previous microbiota studies have led to the presumption that captive animals are poor models for microbial studies in wildlife. Here, we show that colonization of polar bears by Ursidibacter maritimus is unaffected by factors related to captivity, reflecting a deep symbiotic bond to the host. We argue that the study of ecological and evolutionary principles in captive wildlife is possible for host-adapted taxa such as those in the Pasteurellaceae family. Moreover, studying captive, often trained animals protects wild populations from the stress associated with obtaining samples.

Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions

The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.

Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments

Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.

Gut microbiota of animals living in polluted environments are a potential resource of anticancer molecules

Cancer is a prominent cause of morbidity and mortality worldwide, in spite of advances in therapeutic interventions and supportive care. In 2018 alone, there were 18·1 million new cancer cases and 9·6 million deaths indicating the need for novel anticancer agents. Plant-based products have often been linked with protective effects against communicable and non-communicable diseases. Recently, we have shown that animals such as crocodiles thrive in polluted environments and are often exposed to carcinogenic agents, but still benefit from prolonged lifespan. The protective mechanisms shielding them from cancer could be attributed to the immune system, and/or it is possible that their gut microbiota produce anticancer molecules. In support, several lines of evidence suggest that gut microbiota plays a critical role in the physiology of its host. Here, we reviewed the available literature to assess whether the gut microbiota of animals thriving in polluted environment possess anticancer molecules.

Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents

Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gut microbiota of free-ranging barn swallows (Hirundo rustica) by studying co-occurring migrant and resident subspecies sampled during the autumn migration at a migratory bottleneck. We found that within-host microbial richness (α-diversity) was similar between migrant and resident microbial communities. In contrast, we found that microbial communities (β-diversity) were significantly different between groups regarding both microbes present and their relative abundances. Compositional differences were found for 36 bacterial genera, with 27 exhibiting greater abundance in migrants and nine exhibiting greater abundance in residents. There was heightened abundance of Mycoplasma spp. and Corynebacterium spp. in migrants, a pattern shared by other studies of migratory species. Screens for key regional pathogens revealed that neither residents nor migrants carried avian influenza viruses and Newcastle disease virus, suggesting that the status of these diseases did not underlie observed differences in microbiome composition. Furthermore, the prevalence and abundance of Salmonella spp., as determined from microbiome data and cultural assays, were both low and similar across the groups. Overall, our results indicate that microbial composition differs between migratory and resident barn swallows, even when they are conspecific and sympatrically occurring. Differences in host origins (breeding sites) may result in microbial community divergence, and varied behaviours throughout the annual cycle (e.g., migration) could further differentiate compositional structure as it relates to functional needs.

The potential role of the gut microbiota in shaping host energetics and metabolic rate

It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.

Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.

Metabolomic LC-MS/MS analyses and meta 16S rRNA gene analyses on cecal feces of Japanese rock ptarmigans reveal fundamental differences between semi-wild and captive raised individuals

Ex situ conservation of Japanese rock ptarmigans began in 2015 with the aim of reintroducing artificially raised birds into their original habitat. However, the current raising method in captivity seems insufficient in terms of the survivability of artificially raised birds in natural conditions. Feeding management is one potential reason for such insufficiency. In this study, we performed a comprehensive analysis of the hydrophilic metabolites by LC-MS/MS for the cecal feces of Japanese rock ptarmigans under in situ and ex situ conservation to reveal their gut chemical environment. We also analyzed the developmental processes of cecal microbiomes both in situ semi-wild and ex situ captive individuals. Metabolites of nucleic acid were rich in the in situ individuals, and free amino acids were rich in the ex situ individuals. The differences in the microbiome composition between in situ and ex situ individuals were also pronounced; major genera of in situ individuals were not detected or few in ex situ individuals. The alpha diversity of the cecal microbiome of semi-wild chicks at 1 week of age was almost the same as that of their hens, while it was very low in captive individuals. Sub-therapeutic use of oxytetracycline, a diet rich in protein and energy, and isolation from adult birds are considered to be causes for these great differences in gut chemical and microbiological environment between in situ and ex situ individuals.

Marsupial Gut Microbiome

The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.

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.

Captivity Influences Gut Microbiota in Crocodile Lizards (Shinisaurus crocodilurus)

Captivity is an important measure for conservation of an endangered species, and it is becoming a hot topic in conservation biology, which integrates gut microbiota and endangered species management in captivity. As an ancient reptile, the crocodile lizard (Shinisaurus crocodilurus) is facing extreme danger of extinction, resulting in great significance to species conservation in the reserve. Thus, it is critical to understand the differences in gut microbiota composition between captive and wild populations, as it could provide fundamental information for conservative management of crocodile lizards. Here, fecal samples of crocodile lizards were collected from two wild and one captive populations with different ages (i.e., juveniles and adults) and were analyzed for microbiota composition by 16S ribosomal RNA (rRNA) gene amplicon sequencing. This study showed that the lizard gut microbiota was mainly composed of Firmicutes and Proteobacteria. The gut microbiota composition of crocodile lizard did not differ between juveniles and adults, as well as between two wild populations. Interestingly, captivity increased community richness and influenced community structures of gut microbiota in crocodile lizards, compared with wild congeners. This was indicated by higher abundances of the genera Epulopiscium and Glutamicibacter. These increases might be induced by complex integration of simple food resources or human contact in captivity. The gut microbiota functions of crocodile lizards are primarily enriched in metabolism, environmental information processing, genetic information processing, and cellular processes based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This study provides fundamental information about the gut microbiota of crocodile lizards in wild and captive populations. In the future, exploring the relationship among diet, gut microbiota, and host health is necessary for providing animal conservation strategies.

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.