Spatial heterogeneity of the shorebird gastrointestinal microbiome

Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks

In this study, we sought to determine the effects of intestinal flora on the feed efficiency of meat ducks by evaluating the correlation between intestinal flora and residual feed intake. The F2 generation of Cherry Valley ducks × Runzhou Crested White ducks was used as the study subjects, and feed consumption being recorded from d 21 to 42. RFI was calculated based on growth performance, and 20 low RFI and 20 high RFI ducks were randomly selected to characterize the effect of RFI on growth performance. To analyze the intestinal flora affecting RFI, 16s rDNA sequencing was performed on the contents of 5 intestinal segments from the HR and LR groups, and macrogenomic sequencing was performed on the cecal contents. Feed intake, average daily feed intake, feed conversion ratio, and residual feed intake were lower in low RFI. Analysis of the intestinal flora revealed the cecum to be more highly enriched in the carbohydrate metabolism pathway and less enriched with potentially pathogenic taxa than the other assessed intestinal regions. Further analysis of the cecal microbiota identified nine significantly differentially enriched intestinal flora. In this study, we accordingly identified a basis for the mechanisms underlying the effects of the intestinal flora on meat duck feed efficiency.

Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time

Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.

Comparative analysis of two nonlethal methods for the study of the gut bacterial communities in wild lizards

Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons, but it remains unclear which nonlethal methods provide more accurate information about gut microbiota. We compared the bacterial communities of three gastrointestinal tract (GIT) segments, that is, stomach, small intestine (midgut), and rectum (hindgut) with the bacterial communities of the cloaca and feces in the mesquite lizard Sceloporus grammicus. The hindgut had the highest taxonomic and functional alpha diversity, followed by midgut and feces, whereas the stomach and cloaca showed the lowest diversities. The taxonomic assemblages of the GIT segments at the phylum level were strongly correlated with those retrieved from feces and cloacal swabs (rs > 0.84 in all cases). The turnover ratio of Amplicon Sequence Variants (ASVs) between midgut and hindgut and the feces was lower than the ratio between these segments and the cloaca. More than half of the core-ASVs in the midgut (24 of 32) and hindgut (58 of 97) were also found in feces, while less than 5 were found in the cloaca. At the ASVs level, however, the structure of the bacterial communities of the midgut and hindgut were similar to those detected in feces and cloaca. Our findings suggest that fecal samples and cloacal swabs of spiny lizards provide a good approximation of the taxonomic assemblages and beta diversity of midgut and hindgut microbiota, while feces better represent the bacterial communities of the intestinal segments at a single nucleotide variation level than cloacal swabs.

Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds

The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.

Aedes albopictus microbiome derives from environmental sources and partitions across distinct host tissues

The mosquito microbiome consists of a consortium of interacting microorganisms that reside on and within culicid hosts. Mosquitoes acquire most of their microbial diversity from the environment over their life cycle. Once present within the mosquito host, the microbes colonize distinct tissues, and these symbiotic relationships are maintained by immune-related mechanisms, environmental filtering, and trait selection. The processes that govern how environmental microbes assemble across the tissues within mosquitoes remain poorly resolved. We use ecological network analyses to examine how environmental bacteria assemble to form bacteriomes among Aedes albopictus host tissues. Mosquitoes, water, soil, and plant nectar were collected from 20 sites in the Mānoa Valley, Oahu. DNA was extracted and associated bacteriomes were inventoried using Earth Microbiome Project protocols. We find that the bacteriomes of A. albopictus tissues were compositional taxonomic subsets of environmental bacteriomes and suggest that the environmental microbiome serves as a source pool that supports mosquito microbiome diversity. Within the mosquito, the microbiomes of the crop, midgut, Malpighian tubules, and ovaries differed in composition. This microbial diversity partitioned among host tissues formed two specialized modules: one in the crop and midgut, and another in the Malpighian tubules and ovaries. The specialized modules may form based on microbe niche preferences and/or selection of mosquito tissues for specific microbes that aid unique biological functions of the tissue types. A strong niche-driven assembly of tissue-specific microbiotas from the environmental species pool suggests that each tissue has specialized associations with microbes, which derive from host-mediated microbe selection.

Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover

Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds. IMPORTANCE Many animals migrate long distances annually, and these journeys require intense physiological and morphological adaptations. One such adaptation in shorebirds is the ability to rapidly gain weight at stopover locations in the middle of their migrations. The role of the microbiome in weight gain in birds is unresolved but is likely to play a role. Here, we collected 100 fecal samples from Ruddy Turnstones to investigate microbiome composition (who is there) and function (what they are doing) during stopover weight gain in Delaware Bay, USA. Using multiple molecular methods, we show that both taxonomic composition and function of the microbiome shifts during weight gain. We identified 10 genes that are associated with weight class, and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.

Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird

Background

The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela.

Methods

Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO.

Results

The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences.

Conclusion

Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.

Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches

The taxonomic structure of microbial community sample is highly habitat-specific, making source tracking possible, allowing identification of the niches where samples originate. However, current methods face challenges when source tracking is scaled up. Here, we introduce a deep learning method based on the Ontology-aware Neural Network approach, ONN4MST, for large-scale source tracking. ONN4MST outperformed other methods with near-optimal accuracy when source tracking among 125,823 samples from 114 niches. ONN4MST also has a broad spectrum of applications. Overall, this study represents the first model-based method for source tracking among sub-million microbial community samples from hundreds of niches, with superior speed, accuracy, and interpretability. ONN4MST is available at https://github.com/HUST-NingKang-Lab/ONN4MST.

Specific gut bacterial responses to natural diets of tropical birds

The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.

Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor)

Simple Summary

The different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut microbiota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in different parts of the lizards’ intestine.

Abstract

Vertebrates maintain complex symbiotic relationships with microbiota living within their gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and their gut microbiota. However, this understanding is limited in lizards and the spatial heterogeneity and co-occurrence patterns of gut microbiota inside the gastrointestinal tracts of a host and variations of microbial community among samples remain poorly understood. To address this issue and provide a guide for gut microbiota sampling from lizards, we investigated the bacteria in three gut locations of the oriental garden lizard (Calotes versicolor) and the data were analyzed for bacterial composition by 16S ribosomal RNA (16S rRNA) gene amplicon sequencing. We found the relative abundance of the dominant phyla exhibited an increasing trend from the small intestine to the large intestine, and phyla Firmicutes, Bacteroidetes and Proteobacteria were the three primary phyla in the gut microbiota of C. versicolor. There were a higher abundance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the sample from the hindgut. The secondary bile acid biosynthesis, glycosaminoglycan degradation, sphingolipid metabolism and lysosome were significantly higher in the hindgut than that in the small intestine. Taken together our results indicate variations of gut microbiota composition and metabolic pathway in different parts of the oriental garden lizard.

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels

Background

Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) are obligate hibernators and are only active 4–5 months annually. During this period, squirrels rapidly acquire fat for use during hibernation. We investigated how the gut microbiome changed over the active season in the mucosa and lumen of two gut sections: the cecum and ileum. We sequenced the 16S rRNA gene to assess diversity and composition of the squirrel gut microbiome and used differential abundance and network analyses to identify relationships among gut sections.

Results

Microbial composition significantly differed between the cecum and ileum, and within the ileum between the mucosa and lumen. Cecum mucosa and lumen samples did not differ in alpha diversity and composition, and clustered by individual squirrel. Ileum mucosa and lumen samples differed in community composition, which can likely be attributed to the transient nature of food-associated bacteria in the lumen. We did not detect a shift in microbiome diversity and overall composition over the duration of the active season, indicating that the squirrel microbiome may be relatively robust to changes in physiology.

Conclusions

Overall, we found that the 13-lined ground squirrel microbiome is shaped by microenvironment during the active season. Our results provide baseline data for new avenues of research, such as investigating potential differences in microbial function among these physiologically unique gut environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00117-0.

Avian gut microbiomes taking flight

Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.

Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

Human activities shape resources available to wild animals, impacting diet and probably altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analysing the effect of artificially supplemented food provided as part of a crane-agriculture management programme. We sampled faecal droppings in Russia (nonsupplemented, premigration) and in Israel in late autumn (nonsupplemented, postmigration) and winter (supplemented and nonsupplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from nonsupplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the nonsupplemented groups spent most of their time in agricultural fields, probably feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, nonsupplemented and food-supplemented diets probably diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in nonsupplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behaviour towards understanding how human-induced changes shape the gut microbiota in wild animals.

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens

BACKGROUND

Feed contributes most to livestock production costs. Improving feed efficiency is crucial to increase profitability and sustainability for animal production. Host genetics and the gut microbiota can both influence the host phenotype. However, the association between the gut microbiota and host genetics and their joint contribution to feed efficiency in chickens is largely unclear.

RESULTS

Here, we examined microbial data from the duodenum, jejunum, ileum, cecum, and feces in 206 chickens and their host genotypes and confirmed that the microbial phenotypes and co-occurrence networks exhibited dramatic spatial heterogeneity along the digestive tract. The correlations between host genetic kinship and gut microbial similarities within different sampling sites were weak, with coefficients ranging from - 0.07 to 0.08. However, microbial genome-wide analysis revealed that genetic markers near or inside the genes MTHFD1L and LARGE1 were associated with the abundances of cecal Megasphaera and Parabacteroides, respectively. The effect of host genetics on residual feed intake (RFI) was 39%. We further identified three independent genetic variations that were related to feed efficiency and had a modest effect on the gut microbiota. The contributions of the gut microbiota from the different parts of the intestinal tract on RFI were distinct. The cecal microbiota accounted for 28% of the RFI variance, a value higher than that explained by the duodenal, jejunal, ileal, and fecal microbiota. Additionally, six bacteria exhibited significant associations with RFI. Specifically, lower abundances of duodenal Akkermansia muciniphila and cecal Parabacteroides and higher abundances of cecal Lactobacillus, Corynebacterium, Coprobacillus, and Slackia were related to better feed efficiency.

CONCLUSIONS

Our findings solidified the notion that both host genetics and the gut microbiota, especially the cecal microbiota, can drive the variation in feed efficiency. Although host genetics has a limited effect on the entire microbial community, a small fraction of gut microorganisms tends to interact with host genes, jointly contributing to feed efficiency. Therefore, the gut microbiota and host genetic variations can be simultaneously targeted by favoring more-efficient taxa and selective breeding to improve feed efficiency in chickens. Video abstract.

Gut microbiome of migratory shorebirds: Current status and future perspectives

Migratory shorebirds have many unique life history characteristics, such as long-distance travel between breeding sites, stopover sites, and wintering sites. The physiological challenges for migrant energy requirement and immunity may affect their gut microbiome community. Here, we reviewed the specific features (e.g., relatively high proportion of Corynebacterium and Fusobacterium) in the gut microbiome of 18 migratory shorebirds, and the factors (e.g., diet, migration, environment, and phylogeny) affecting the gut microbiome. We discussed possible future studies of the gut microbiome in migratory shorebirds, including the composition and function of the spatial-temporal gut microbiome, and the potential contributions made by the gut microbiome to energy requirement during migration.