Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests

Seasonal variation in gut microbiota of migratory wild raptors: a case study in white-tailed eagles

BACKGROUND

Migration poses significant energetic challenges for migratory birds, during which both intrinsic and extrinsic factors affecting the gut microbiota alter substantially. While the temporal dynamics of gut microbiota in wild birds across migration seasons have garnered increasing attention, research on the seasonal variation in wild raptors remains limited despite their distinct gut microbiota structures. Furthermore, raptors, being the highest trophic level in the food chain, have been found to harbor more pathogens and antibiotic resistance genes (ARGs). In this study, we characterized the diversity and composition of the gut microbiota of wild white-tailed eagles at a critical stopover site along the East Asian Flyway (EAF). Fecal samples were collected during both autumn and spring migration seasons and microbial compositions were analyzed using high-throughput sequencing.

RESULTS

The most prevalent bacterial phylum in the gut microbiome of white-tailed eagles during both migration seasons was Firmicutes. The diversity of the gut microbiota is elevated in the spring migration season and the bacterial community composition significantly differed between two seasons. Individuals in spring migration show elevated levels of Clostridium_sensu_stricto_13 and Brochothrix, most likely related to the consumption of carrion. Conversely, individuals in autumn migration showed a higher prevalence of potential pathogens such as Fusobacterium and Escherichia-Shigella. Furthermore, we found that specific genera were seasonally enriched, probably reflecting distinct environmental exposures along migration routes.

CONCLUSIONS

This study revealed substantial seasonal variation in the gut microbiota of migratory white-tailed eagles, most likely shaped by dietary shifts, environmental factors, and physiological stress during migration. The higher prevalence of pathogens during autumn migration highlights potential health risks for eagles and their ecosystems, emphasizing the need for targeted conservation strategies at stopover sites. These findings contribute to understanding the dynamic interactions between migration and gut microbiota in wild raptors and provide valuable insights into their ecological and health management. While dietary differences may play a role, further research is needed to directly assess their impact.

Little Peacemakers: Microbes Can Promote Nonviolent Conflict Resolution by Their Hosts

Conflicts between individuals of the same species are common in nature and are mostly resolved with limited aggression. Several theoretical studies, such as the Hawk-Dove (HD) game model, investigate the evolution of limited aggression expressed during conflicts between individuals. These studies mainly focus on the individuals involved in the conflict and their genes. Recently accumulating evidence indicates that microbes are associated with diverse functions of their host and can affect host behavior. Here we extend the classic HD game model to include both the hosts and their microbes, examining how natural selection acts on the microbes. We find that nonaggressive host behavior is more likely to evolve and spread in a population when induced by the microbes residing in the host, compared to nonaggressive behavior induced by host genes. Horizontal transmission allows microbes to colonize new hosts, making their success dependent on the fitness of both the host and its opponent. Therefore, selection on the microbes favors reduced host aggressiveness under wider conditions compared to selection acting on genes alone. Our results suggest that microbes may help explain the ubiquity of nonviolent conflict resolution. Consequently, factors that alter the microbial composition within hosts may affect the aggressiveness level in host populations.

The gut microbiota of three avian species living in sympatry

BACKGROUND

Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

RESULTS

We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

CONCLUSION

While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.

Effects of parental care on skin microbial community composition in poison frogs

Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects. Early exposure to microbes can have lasting influences on the assembly and functionality of the host's microbiota, leaving a life-long imprint on host health and disease. Studies of the role played by parental care in microbial acquisition have primarily focused on humans and hosts with agricultural relevance. Anuran vertebrates offer the opportunity to examine microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of microbiota during parental care in a poison frog (Family Dendrobatidae), where fathers transport their offspring piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of the embryo begins after hatching from the vitelline envelope, emphasizing its potential role as microbial barrier during early development. Using a laboratory cross-foster experiment, we demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled frogs and tadpoles of sympatric species that do or do not exhibit tadpole transport in their natural habitat. We found more diverse microbial communities associated with tadpoles of transporting species compared to a non-transporting frog. However, we detected no difference in the degree of similarity between adult and tadpole skin microbiotas, based on whether the frog species exhibits transporting behavior or not. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low prevalence. This is the first study to describe vertical transmission of skin microbes in anuran amphibians, showing that offspring transport may serve as a mechanism for transmission of parental skin microbes. Overall, these findings provide a foundation for further research on how vertical transmission in this order impacts host-associated microbiota and physiology.

Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds

Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.

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.

Early-life factors shaping the gut microbiota of Common buzzard nestlings

BACKGROUND

Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.

RESULTS

We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.

CONCLUSION

Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.

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.

Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes

Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.

Symbiotic Synergy from Sponges to Humans: Microflora-Host Harmony Is Crucial for Ensuring Survival and Shielding against Invading Pathogens

Gut microbiota plays several roles in the host organism's metabolism and physiology. This phenomenon holds across different species from different kingdoms and classes. Different species across various classes engage in continuous crosstalk via various mechanisms with their gut microbiota, ensuring homeostasis of the host. In this Review, the diversity of the microflora, the development of the microflora in the host, its regulations by the host, and its functional implications on the host, especially in the context of dysbiosis, are discussed across different organisms from sponges to humans. Overall, our review aims to address the indispensable nature of the microbiome in the host's survival, fitness, and protection against invading pathogens.

Nearly (?) sterile avian egg in a passerine bird

During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity, and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonized after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate the contribution of these mechanisms to gut microbiota formation in avian embryos. We investigated microbiome of the egg content (day 0; E0-egg), embryonic gut at day 13 (E13) and female faeces in a free-living passerine, the great tit (Parus major), using a methodologically advanced procedure combining 16S rRNA gene sequencing and microbe-specific qPCR assays. Our metabarcoding revealed that the avian egg is (nearly) sterile, but acquires a slightly richer microbiome during the embryonic development. Of the three potentially pathogenic bacteria targeted by qPCR, only Dietzia was found in E0-egg (yet also in negative controls), E13 gut and female samples, which might indicate possible vertical transfer. Unlike in poultry, we have shown that major bacterial colonization of the gut in passerines does not occur before hatching. We emphasize that protocols that carefully check for environmental contamination are critical in studies with low-bacterial biomass samples.

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations

BACKGROUND

Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails.

RESULTS

We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments.

CONCLUSIONS

Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.

Responses of the gut microbiota to environmental heavy metal pollution in tree sparrow (Passer montanus) nestlings

Gut microbiota plays a critical role in regulating the health and adaptation of wildlife. However, our understanding of how exposure to environmental heavy metals influences the gut microbiota of wild birds, particularly during the vulnerable and sensitive nestling stage, remains limited. In order to investigate the relationship between heavy metals and the gut microbiota, we analyzed the characteristics of gut microbiota and heavy metals levels in tree sparrow nestlings at different ages (6, 9 and 12-day-old). The study was conducted in two distinct areas: Baiyin (BY), which is heavily contaminated with heavy metals, and Liujiaxia (LJX), a relatively unpolluted area. Our result reveled a decrease in gut microbiota diversity and increased inter-individual variation among nestlings in BY. However, we also observed an increase in the abundance of bacterial groups and an up-regulation of bacterial metabolic functions associated with resistance to heavy metals toxicity in BY. Furthermore, we identified a metal-associated shift in the relative abundance of microbial taxa in 12-day-old tree sparrow nestlings in BY, particularly involving Aeromonadaceae, Ruminococcaceae and Pseudomonadaceae. Moreover, a significant positive correlation was found between the body condition of tree sparrow nestlings and the abundance of Bifidobacteriaceae in BY. Collectively, our findings indicate that the gut microbiota of tree sparrow nestlings is susceptible to heavy metals during early development. However, the results also highlight the presence of adaptive responses that enable them to effectively cope with environmental heavy metal pollution.

Role of gut microbiota in the postnatal thermoregulation of Brandt's voles

Homeothermy is crucial for mammals. Postnatal growth is the key period for young offspring to acquire gut microbiota. Although gut microbiota may affect mammal thermogenesis, the impact of developmental regulation of gut microbiota on the ability of young pups to produce heat remains unclear. Antibiotics were used to interfere with the establishment of gut microbiota during the development of Brandt's voles, and their thermogenic development and regulatory pathways were determined. Deprivation of microbiota by antibiotics inhibits the development of thermogenesis in pups. Butyric acid and bile acid, as metabolites of gut microbiota, participated in the thermoregulation of pups. We propose that gut microbiota promote the development of thermoregulation through the butyric acid-free fatty acid receptor-2-uncoupling protein-1 or the deoxycholic acid-Takeda-G-protein-receptor-5-uncoupling protein-1 pathway in pups. These results show a relationship between gut microbiota and thermogenesis and expand the mechanism of postnatal development of thermogenesis in small mammals.

The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota

The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: (1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? (2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? (3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.

Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle

Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.

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

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

The abundance and diversity of antibiotic resistance genes in layer chicken ceca is associated with farm enviroment

Industrialized layer chicken feedlots harbor complex environmental microbial communities that affect the enrichment and exchange of gut bacteria and antibiotic resistance genes (ARGs). However, the contribution of different environmental sources to the gut ARGs of layer chickens is not clear. Here, layer chicken gut and environmental samples (air, water, feed, cage, feather, maternal hen feces, uropygial glands) were collected during the early 3 month period before the laying of eggs, and the source and characteristics of the gut microorganisms and ARGs were analyzed by performing 16S rRNA and metagenomic sequencing. The results showed that the abundances of Bacteroidetes and Actinobacteria in cecum of layer chickens gradually increased, while that of Proteobacteria decreased with age, and the number and relative abundance of ARGs decreased significantly with age. On day 5, 57% of the layer chicken cecal ARGs were from feather samples, and 30% were from cage samples. Subsequently, the contribution of cage ARGs became progressively more prominent over time. At days 30 and 57, the contribution of cage ARGs to the chick cecal ARGs reached 63.3 and 69.5%, respectively. The bacterial community composition (especially the abundances of Klebsiella pneumoniae and Escherichia coli) was the major factor impacting the ARG profile. K. pneumoniae and E. coli were mainly transmitted from feathers to the layer chicken cecum, and the contribution rates were 32 and 3.4%, respectively. In addition, we observed the transmission of ARG-carrying bacteria (Bacteroides fragilis) from the cage to the gut, with a contribution rate of 11.5%. It is noteworthy that B. fragilis is an opportunistic pathogen that may cause diarrhea in laying hens. These results can provide reference data for the healthy breeding of layer chickens and the prevention and control of ARG pollution.

Fermented Bamboo Fiber Improves Productive Performance by Regulating Gut Microbiota and Inhibiting Chronic Inflammation of Sows and Piglets during Late Gestation and Lactation

Sows exhibit metabolic syndrome and significant changes in intestinal microbiota during late gestation and lactation, affecting sow performance and piglet health. Dietary fiber (DF) is widely applied to improve sow performance by modulating gut microbiota and their by-products. Here, 60 sows were randomly allocated to groups, including CON (8% wheat bran), FBF-1 (1% fermented bamboo fiber), FBF-2 (2.5% fermented bamboo fiber), and FBF-3 (4% fermented bamboo fiber) from day 80 of gestation (G80d) to the end of lactation (L21d). Compared with CON, the FBF-3 diet decreased lactation backfat loss, increased average daily feed intake (ADFI) during lactation, and the weight gain of piglets, while supplementation of FBF increased fecal water content and reduced the rate of constipation in sows. Further, the yield and quality of milk of sows in FBF groups were improved. The FBF-3 diet significantly reduced markers of intestinal permeability (diamine oxidase and endotoxin) and systemic inflammation (interleukin-6 [IL-6] and tumor necrosis factor alpha) in sow serum during lactation, while it increased the anti-inflammatory marker (IL-10). Similarly, the piglets in the FBF-2 and FBF-3 groups had lower levels of IL-6 and higher levels of IgG, IgM, and insulin-like growth factor in serum. In addition, sows fed the 4% FBF diet had higher levels of acetate, propionate, butyrate, and total short-chain fatty acids (SCFAs) in feces than CON, and total SCFAs were promoted in piglets from the FBF-3 group. Spearman correlation analysis showed that immunity, inflammation, and intestinal microbiota are closely related to sow performance, which can affect piglet growth. The potential mechanism could be that FBF promoted the enrichment of beneficial genera such as Lachnospira, Lachnospiracea_XPB1014_Group, and Roseburia and the production of SCFAs in the sow's intestine, and reduced the relative abundance of harmful bacteria such as Fusobacterium, Sutterellaceae, and Sutterella. Meanwhile, the intake of FBF by sows affected the gut microbial composition of their offspring piglets, significantly increasing the relative abundance of beneficial bacteria Alistipes and Lachnoclostridium and decreasing the relative abundance of pathogenic bacteria Trueperella among colonic microorganisms. IMPORTANCE Dietary fiber is widely applied in the nutrition of sows due to its potential value in improving performance and intestinal health. Fermented bamboo fiber, rich in dietary fiber, has not been fully evaluated to be used in sow diets. Sows mobilize body reserves during gestation and lactation due to nutrients being prioritized for lactation purposes while feeding piglets, which generally leads to metabolism and immunity undergoing drastic changes. The main manifestations are increased inflammation and intestinal permeability and disturbed intestinal flora, which ultimately reduces the ADFI and milk quality, thus affecting the growth of piglets. The study described here is the first attempt to provide FBF for sows in late gestation and lactation can reverse this process. The 4% FBF was initially explored to have the most significantly beneficial effect. It provides a potentially effective method for dietary modification to control the gut microbiota and its metabolites to improve sow and piglet health. Moreover, the sow-piglet model offers a reference for investigating the impact of dietary fiber on the intestinal health of human mothers and infants.

Parental care contributes to vertical transmission of microbes in a skin-feeding and direct-developing caecilian

BACKGROUND

Our current understanding of vertebrate skin and gut microbiomes, and their vertical transmission, remains incomplete as major lineages and varied forms of parental care remain unexplored. The diverse and elaborate forms of parental care exhibited by amphibians constitute an ideal system to study microbe transmission, yet investigations of vertical transmission among frogs and salamanders have been inconclusive. In this study, we assess bacteria transmission in Herpele squalostoma, an oviparous direct-developing caecilian in which females obligately attend juveniles that feed on their mother's skin (dermatophagy).

RESULTS

We used 16S rRNA amplicon-sequencing of the skin and gut of wild caught H. squalostoma individuals (males, females, including those attending juveniles) as well as environmental samples. Sourcetracker analyses revealed that juveniles obtain an important portion of their skin and gut bacteria communities from their mother. The contribution of a mother's skin to the skin and gut of her respective juveniles was much larger than that of any other bacteria source. In contrast to males and females not attending juveniles, only the skins of juveniles and their mothers were colonized by bacteria taxa Verrucomicrobiaceae, Nocardioidaceae, and Erysipelotrichaceae. In addition to providing indirect evidence for microbiome transmission linked to parental care among amphibians, our study also points to noticeable differences between the skin and gut communities of H. squalostoma and that of many frogs and salamanders, which warrants further investigation.

CONCLUSION

Our study is the first to find strong support for vertical bacteria transmission attributed to parental care in a direct-developing amphibian species. This suggests that obligate parental care may promote microbiome transmission in caecilians.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Microbial diversity and community composition of fecal microbiota in dual-purpose and egg type ducks

Introduction

Ducks are important agricultural animals, which can be divided into egg and dual-purpose type ducks according to economic use. The gut microbiota of ducks plays an important role in their metabolism, immune regulation, and health maintenance.

Methods

Here, we use 16S rDNA V4 hypervariable amplicon sequencing to investigate the compositions and community structures of fecal microbiota between egg (five breeds, 96 individuals) and dual-purpose type ducks (four breeds, 73 individuals) that were reared under the same conditions.

Results

The alpha diversity of fecal microflora in egg type ducks was significantly higher than that in dual-type ducks. In contrast, there is no significant difference in the fecal microbial community richness between the two groups. MetaStat analysis showed that the abundance of Peptostreptococcaceae, Streptococcaceae, Lactobacillus, Romboutsia, and Campylobacter were significantly different between the two groups. The biomarkers associated with the egg and dual-purpose type ducks were identified using LEfSe analysis and IndVal index. Function prediction of the gut microbiota indicated significant differences between the two groups. The functions of environmental information processing, carbohydrate metabolism, lipid metabolism, xenobiotic biodegradation and metabolism, and metabolism of terpenoids and polyketides were more abundant in egg type ducks. Conversely, the genetic information processing, nucleotide metabolism, biosynthesis of amino acids and secondary metabolites, glycan biosynthesis and metabolism, fatty acid elongation, and insulin resistance were significantly enriched in dual-purpose type ducks.

Discussion

This study explored the structure and diversity of the gut microbiota of ducks from different economic-use groups, and provides a reference for improving duck performance by using related probiotics in production.

Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens

BACKGROUND

Nutrition drives immunity and health in animals, and maternal immunity benefits offspring. In our previous study, a nutritional intervention strategy was found to promote the immunity of hens, which subsequently improved immunity and growth in offspring chicks. Maternal effects clearly exist, but how are mothers' immune advantages transferred to their offspring, and how do they benefit them?

RESULTS

Here, we traced the beneficial effects back to the process of egg formation in the reproductive system, and we focused on the embryonic intestinal transcriptome and development, as well as on maternal microbial transfer in offspring. We found that maternal nutritional intervention benefits maternal immunity, egg hatching, and offspring growth. The results of protein and gene quantitative assays showed that the transfer of immune factors into egg whites and yolks depends on maternal levels. Histological observations indicated that the promotion of offspring intestinal development begins in the embryonic period. Microbiota analyses suggested that maternal microbes transfer to the embryonic gut from the magnum to the egg white. Transcriptome analyses revealed that offspring embryonic intestinal transcriptome shifts are related to development and immunity. Moreover, correlation analyses showed that the embryonic gut microbiota is correlated with the intestinal transcriptome and development.

CONCLUSIONS

This study suggests that maternal immunity positively influences offspring intestinal immunity establishment and intestinal development beginning in the embryonic period. Adaptive maternal effects might be accomplished via the transfer of relatively large amounts of maternal immune factors and by shaping of the reproductive system microbiota by strong maternal immunity. Moreover, reproductive system microbes may be useful resources for the promotion of animal health. Video Abstract.

Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves

Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.

Intestinal Microbiota of Anser fabalis Wintering in Two Lakes in the Middle and Lower Yangtze River Floodplain

The intestinal microbiota of migratory birds participate in the life activities of the host and are affected by external environmental factors. The difference in habitat environment provides diversity in external environmental selection pressure for the same overwintering waterfowl, which may be reflected in their intestinal microbiota. Caizi lake and Shengjin Lake in the Middle and Lower Yangtze River Floodplain are the main habitats for migratory waterfowl in winter, especially the Anser fabalis (A. fabalis). It is important to explore the changes in intestinal microbiota composition and function of A. fabalis in the early overwintering period to clarify the effect of habitat size and protection status on intestinal microbiota. In this study, the composition and structural characteristics of the intestinal microbiota of A. fabalis in Shengjin Lake (SL) and Caizi Lake (CL) were preliminarily explored in order to obtain data for the migratory birds. In both SL and CL groups, 16S rRNA amplicon sequencing analysis showed that Firmicutes was the dominant bacterial phylum, but the relative abundance showed significant differences. Lactobacillus was the most abundant genus in both SL and CL groups. At the species level, the abundance of L. aviaries was the highest, with a relative abundance in both SL and CL groups of more than 34%. When comparing the average relative abundance of the 15 most abundant genera, it was found that Subdoligranulum, Exiguobacterium, and Terrisporobacter had higher abundances in the intestinal microbiota of CL A. fabalis, while Streptococcus and Rothia had higher abundances in the intestinal microbiota of SL A. fabalis. There was only a positive correlation between Bacteroidota and Proteobacteria in the intestinal microbiota flora of SL A. fabalis, and the species were closely related. At the same time, there were positive and negative correlations between Firmicutes and Actinomycetes. However, CL is mainly associated with a positive correlation between Firmicutes and Actinomycetes, and there are also a small number of connections between Firmicutes. PICRUSt1 prediction analysis revealed that the Clusters of Orthologous Groups (COG) functions of SL and CL involve energy production and transformation, amino acid transport and metabolism, carbohydrate transport and metabolism, and transcription. Understanding the changes in intestinal microbiota in Aves during the overwintering period is of great importance to explore the adaptation mechanism of migratory Aves to the overwintering environment. This work provides basic data for an A. fabalis intestinal microbiota study.

Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota

BACKGROUND

The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these birds over the first 3 months of life. We thus documented the development of the gut microbiota and characterised the relative impacts of the early social environment and host selection due to species-specific characteristics and individual genetic backgrounds across ontogeny by using 16S ribosomal RNA gene sequencing.

RESULTS

The taxonomic composition and community structure of the gut microbiota changed across ontogenetic stages; juvenile zebra finches exhibited higher alpha diversity than adults at the post-breeding stage. Furthermore, in early development, the microbial communities of juveniles raised by conspecific and heterospecific foster parents resembled those of their foster family, emphasising the importance of the social environment. In later stages, the social environment continued to influence the gut microbiota, but host selection increased in importance.

CONCLUSIONS

We provided a baseline description of the developmental succession of gut microbiota in zebra finches and Bengalese finches, which is a necessary first step for understanding the impact of the early gut microbiota on host fitness. Furthermore, for the first time in avian species, we showed that the relative strengths of the two forces that shape the establishment and maintenance of the gut microbiota (i.e. host selection and dispersal from the social environment) change during development, with host selection increasing in importance. This finding should be considered when experimentally manipulating the early-life gut microbiota. Our findings also provide new insights into the mechanisms of host selection. Video Abstract.

Incubation determines favorable microbial communities in Chinese alligator nests

Nest materials are a major heat source due to rotting promoted by microbial activity. Additionally, they are a potential microbial source given their direct contact with eggshells. Microbial dynamics during incubation have been studied in wild birds; however, similar studies in reptiles remain elusive. Here, the study characterized microbial communities in the nest materials of Chinese alligator (Alligator sinensis) using high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) region sequences. The results showed that significant changes in the diversity and structure of microbial communities according to different incubation periods. The diversity and richness of bacterial species increased significantly over time, but the relative abundance of the most dominant bacteria in pre-incubation period, including some pathogenic bacteria, declined after incubation. In contrast, fungal species diversity and richness decreased significantly with time. Additionally, nest material composition significantly influenced microbial community structure rather than species diversity and richness. Notably, the fungal community structure showed a stronger response than bacteria to nest material composition, which varied due to differences in plant litter composition. Our results demonstrate the significant response of microbial community diversity and structure to differences in incubation periods and nest material composition in reptiles. It is further emphasized that the importance of incubation period in the conservation of the Chinese alligator and could inform similar studies in other reptiles and birds.

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.

Mixed-Mode Bacterial Transmission via Eggshells in an Oviparous Reptile Without Parental Care

Symbiotic microorganisms play important roles in maintaining health and facilitating the adaptation of the host. We know little about the origin and transgenerational transmission of symbiotic bacteria, especially in egg-laying species without parental care. Here, we investigated the transmission of bacterial symbionts in the Chinese three-keeled pond turtle (Mauremys reevesii), a species with no post-oviposition parental care, by evaluating contributions from potential maternal and environmental sources to eggshell bacterial communities. Using 16S rRNA amplicon sequencing, we established that the bacterial communities of eggshells were similar to those of the maternal cloaca, maternal skin, and nest soil, but distinct from those of surface soil around nest and pond water. Phylogenetic structure analysis and source-tracking models revealed the deterministic assembly process of eggshell microbiota and high contributions of the maternal cloaca, maternal skin, and nest soil microbiota to eggshell bacterial communities. Moreover, maternal cloaca showed divergent contribution to eggshell microbiota compared with two other main sources in phylogenesis and taxonomic composition. The results demonstrate a mixture of horizontal and vertical transmission of symbiotic bacteria across generations in an oviparous turtle without parental care and provide insight into the significance of the eggshell microbiome in embryo development.

Microhabitat Governs the Microbiota of the Pinewood Nematode and Its Vector Beetle: Implication for the Prevalence of Pine Wilt Disease

Our understanding of environmental acquisition of microbes and migration-related alteration of microbiota across habitats has rapidly increased. However, in complex life cycles, such as for many parasites, exactly how these microbes are transmitted across multiple environments, such as hosts and habitats, is unknown. Pinewood nematode, the causal agent of the globally devastating pine wilt disease, provides an ideal model to study the role of microbiota in multispecies interactions because its successful host invasion depends on the interactions among its vector insects, pine hosts, and associated microbes. Here, we studied the role of bacterial and fungal communities involved in the nematode’s life cycle across different micro- (pupal chamber, vector beetle, and dispersal nematodes) and macrohabitats (geographical locations). We identified the potential sources, selection processes, and keystone taxa involved in the host pine-nematode-vector beetle microbiota interactions. Nearly 50% of the microbiota in vector beetle tracheae and ~60% that of third-stage dispersal juveniles were derived from the host pine (pupal chambers), whereas 90% of bacteria of fourth-stage dispersal juveniles originated from vector beetle tracheae. Our results also suggest that vector beetles’ tracheae selectively acquire some key taxa from the microbial community of the pupal chambers. These taxa will be then enriched in the dispersal nematodes traveling in the tracheae and hence likely transported to new host trees. Taken together, our findings contribute to the critical information toward a better understanding of the role of microbiota in pine wilt disease, therefore aiding the knowledge for the development of future biological control agents.

IMPORTANCE Our understanding of animal microbiota acquisition and dispersal-mediated variation has rapidly increased. In this study, using the model of host pine-pinewood nematode-vector beetle (Monochamus sp.) complex, we disentangled the routes of microbial community assembly and transmission mechanisms among these different participants responsible for highly destructive pine wilt disease. We provide evidence that the microhabitat is the driving force shaping the microbial community of these participants. The microbiota of third-stage dispersal juveniles (L_III) of the nematodes collected around pupal chambers and of vector beetles were mainly derived from the host pine (pupal chambers), whereas the vector-entering fourth-stage dispersal juveniles (L_IV) of the nematodes had the simplest microbiota community, not influencing vector’s microbiota. These findings enhanced our understanding of the variation in the microbiota of plants and animals and shed light on microbiota acquisition in complex life cycles.

Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves

The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves' intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P > 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.

Maternal consumption of a fermented diet protects offspring against intestinal inflammation by regulating the gut microbiota

The neonatal intestinal tract is immature and can be easily infected by pathogens causing inflammation. Maternal diet manipulation is a promising nutritional strategy to enhance the gut health of offspring. A fermented diet is a gut microbiota targeting diet containing live probiotics and their metabolites, which benefit the gut and overall health host. However, it remains unclear how a maternal fermented diet (MFD) affects neonatal intestinal inflammation. Here, in vivo and in vitro models together with multi-omics analysis were applied to investigate the impacts and the underlying mechanism through which an MFD prevents from gut inflammation in neonates. An MFD remarkably improved the performance of both sows and piglets and significantly altered the gut microbiome and milk metabolome of sows. In addition, the MFD significantly accelerated the maturation of the gut microbiota of neonates and increased the abundance of gut Lactobacillus and the microbial functions of amino acid-related enzymes and glucose metabolism on the weaning day. Notably, the MFD reduced susceptibility to colonic inflammation in offspring. The fecal microbiota of sows was then transplanted into mouse dams and it was found that the mouse dams and pups in the MFD group alleviated the LPS-induced decrease in gut Lactobacillus abundance and barrier injury. Milk L-glutamine (GLN) and gut Lactobacillus reuteri (LR) were found as two of the main MFD-induced sow effectors that contributed to the gut health of piglets. The properties of LR and GLN in modulating gut microbiota and alleviating colonic inflammation by inhibiting the phosphorylation of p38 and JNK and activation of Caspase 3 were further verified. These findings provide the first data revealing that an MFD drives neonate gut microbiota development and ameliorates the colonic inflammation by regulating the gut microbiota. This fundamental evidence might provide references for modulating maternal nutrition to enhance early-life gut health and prevent gut inflammation.

Hen raising helps chicks establish gut microbiota in their early life and improve microbiota stability after H9N2 challenge

BACKGROUND

Early gut microbial colonization is important for postnatal growth and immune development of the chicken. However, at present, commercial chickens are hatched and raised without adult hens, thus are cut off from the microbiota transfer between hens and chicks. In this study, we compared the gut microbiota composition between hen-reared and separately reared chicks, and its impact on the resistance to H9N2 avian influenza virus, with the motive of investigating the impact of this cutoff in microbiota transfer.

RESULTS

We used the 16SrRNA sequencing method to assess the composition of the gut microbiota in chicks represented by three hen-reared groups and one separately reared group. We found that the diversity of gut microbes in the chicks from the three hen-reared groups was more abundant than in the separately reared group, both at the phylum and genus levels. Our findings highlight the importance of early parental care in influencing the establishment of gut microbiota in the early life of chicks. SourceTracker analysis showed that the feather and cloaca microbiota of hens are the main sources of gut microbiota of chicks. After H9N2 exposure, the viral infection lasted longer in the separately reared chicks, with the viral titers in their oropharyngeal swabs being higher compared to the hen-reared chicks at day 5 post-infection. Interestingly, our results revealed that the gut microbiota of the hen-reared chicks was more stable after H9N2 infection in comparison to that of the separately reared chicks.

CONCLUSIONS

Microbiota transfer between the hens and their chicks promotes the establishment of a balanced and diverse microbiota in the early life of the chicks and improves microbiota stability after H9N2 challenge. These findings advance our understanding of the protective role of gut microbiota in the early life of chicks and should be instrumental in improving chick rearing in the commercial poultry industry. Video Abstract.

Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System

Simple Summary

Yak (Bos grunniens) is the most economically and culturally important domestic bovine species adapted to the extreme ecological environment of the Qinghai–Tibetan Plateau (QTP), which provides milk, meat, transportation, fuel (yak dung), and wool for local nomads as well as major sources of income. Calves are an important part of the sustainable development of the yak industry on the QTP, and the quality of calf rearing directly determines the production performance of adult animals. Under the traditional grazing management, late weaning (>180 days) of yak calves seriously affects the improvement of their production performance. A comparative study of fecal microbiota dynamics of yak and cattle (Bos taurus) calves in different months after weaning will help to understand the changes in intestinal microbiota structure, and will aid in in improving growth rate and survivability of early weaned calves. Our research will contribute to the development of appropriate strategies to regulate the gut microbiome and thus improve the growth and health of the grazing ruminants on the QTP.

Abstract

Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed.

Temperature-induced changes in egg white antimicrobial concentrations during pre-incubation do not influence bacterial trans-shell penetration but do affect hatchling phenotype in Mallards

Microbiome formation and assemblage are essential processes influencing proper embryonal and early-life development in neonates. In birds, transmission of microbes from the outer environment into the egg’s interior has been found to shape embryo viability and hatchling phenotype. However, microbial transmission may be affected by egg-white antimicrobial proteins (AMPs), whose concentration and antimicrobial action are temperature-modulated. As both partial incubation and clutch covering with nest-lining feathers during the pre-incubation period can significantly alter temperature conditions acting on eggs, we experimentally investigated the effects of these behavioural mechanisms on concentrations of both the primary and most abundant egg-white AMPs (lysozyme and avidin) using mallard (Anas platyrhychos) eggs. In addition, we assessed whether concentrations of egg-white AMPs altered the probability and intensity of bacterial trans-shell penetration, thereby affecting hatchling morphological traits in vivo. We observed higher concentrations of lysozyme in partially incubated eggs. Clutch covering with nest-lining feathers had no effect on egg-white AMP concentration and we observed no association between concentration of egg-white lysozyme and avidin with either the probability or intensity of bacterial trans-shell penetration. The higher egg-white lysozyme concentration was associated with decreased scaled body mass index of hatchlings. These outcomes demonstrate that incubation prior to clutch completion in precocial birds can alter concentrations of particular egg-white AMPs, though with no effect on bacterial transmission into the egg in vivo. Furthermore, a higher egg white lysozyme concentration compromised hatchling body condition, suggesting a potential growth-regulating role of lysozyme during embryogenesis in precocial birds.

Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers

BACKGROUND

The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai'i, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored.

METHODS

We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the 'akikiki (Oreomystis bairdi) and the 'akeke'e (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan.

RESULTS

A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. 'Akikiki had a more diverse microbiome compared to 'akeke'e. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in 'akikiki.

CONCLUSION

'Akikiki and 'akeke'e are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.

Black Soldier Fly (Hermetia illucens) Larvae Meal Modulates Intestinal Morphology and Microbiota in Xuefeng Black-Bone Chickens

The addition of Hermetia illucens larvae meal (HILM) to the feed could contribute to particular antimicrobial and intestinal health in animal husbandry. This study was conducted to investigate the effects of HILM on intestinal morphology and microbial diversity in different intestinal segments of Xuefeng black-bone chickens. All of 432 birds (45 weeks old) were randomly assigned to four equal groups with six replicates and 18 hens in each replicate: (A) basal diet, (B) basal diet with 1% HILM, (C) basal diet with 3% HILM, and (D) basal diet with 5% HILM. The results showed that, compared with the basal diet group, the HILM supplement significantly increased the abundance-based coverage estimator (ACE) and Chao index in cecum (p < 0.05). Diet with 1% HILM significantly increased the villus height (VH) of the duodenum (p < 0.05) and cecum microbial diversity as represented by the Simpson index (p < 0.05). In particular, 1% HILM displayed a markedly increase in the genus unclassified Bacteroidales (cecum, p < 0.05). A basal diet with 3% HILM markedly increased the beneficial genus Romboutsia (jejunum, p < 0.05). Also, principal component analysis (PCA) cluster analysis showed that 3% of HILM was more individual than other groups (p < 0.05). However, 5% HILM decreased the VH and the ratio of villus height to crypt depth (VH/CD) of the jejunum and increased beneficial bacteria such as Staphylococcus (p < 0.05), which was regarded as pathogenetic genera. In conclusion, we found that HILM improved intestinal morphology and increased microbiological diversity and species abundance. Together, dietary supplementation of 1 or 3% HILM might benefit the intestinal morphology and intestinal microbiota of Xuefeng black-bone chicken. However, the addition of 5% HILM could decrease VH and the ratio of VH/CD of the jejunum and increased pathogenetic genera. HILM was an excellent protein substitute for Xuefeng black-bone chickens, which could meet the nutritional requirements under the condition of less feed. These results provide information for HILM meal as an alternative source of soybean meal in Xuefeng black-bone chickens’ feed.

The call of the wild: using non-model systems to investigate microbiome-behaviour relationships

On and within most sites across an animal's body live complex communities of microorganisms. These microorganisms perform a variety of important functions for their hosts, including communicating with the brain, immune system and endocrine axes to mediate physiological processes and affect individual behaviour. Microbiome research has primarily focused on the functions of the microbiome within the gastrointestinal tract (gut microbiome) using biomedically relevant laboratory species (i.e. model organisms). These studies have identified important connections between the gut microbiome and host immune, neuroendocrine and nervous systems, as well as how these connections, in turn, influence host behaviour and health. Recently, the field has expanded beyond traditional model systems as it has become apparent that the microbiome can drive differences in behaviour and diet, play a fundamental role in host fitness and influence community-scale dynamics in wild populations. In this Review, we highlight the value of conducting hypothesis-driven research in non-model organisms and the benefits of a comparative approach that assesses patterns across different species or taxa. Using social behaviour as an intellectual framework, we review the bidirectional relationship between the gut microbiome and host behaviour, and identify understudied mechanisms by which these effects may be mediated.

The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch

Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.

Composition and Potential Function of Fecal Bacterial Microbiota from Six Bird Species

Gut microbial communities play a fundamental role in health and disease, but little is known about the gut microbiota of pet bird species. This is important to better understand the impact of microbes on birds’ health but may also be relevant in a context of zoonoses. Total genomic DNA samples from pooled fecal samples from 30 flocks (4–7 pet birds per flock) representing over 150 birds of six different species (two Passeriformes: Northern Mockingbird (Mimus polyglottos) and Zebra Finch (Taeniopygia guttata), and four Psittaciformes: Lovebird (Agapornis, different species), Cockatiel (Nymphicus hollandicus), Red-rumped Parrot (Psephotus haematonotus), and Rose-ringed Parakeet (Psittacula krameri) were used for 16S rRNA gene analysis. Several taxa were found to be different among the bird species (e.g., lowest median of Lactobacillus: 2.2% in Cockatiels; highest median of Lactobacillus: 79.4% in Lovebirds). Despite marked differences among individual pooled samples, each bird species harbored a unique fecal bacterial composition, based on the analysis of UniFrac distances. A predictive approach of metagenomic function and organism-level microbiome phenotypes revealed several differences among the bird species (e.g., a higher proportion of proteobacteria with the potential to form biofilms in samples from Northern Mockingbirds). The results provide a useful catalog of fecal microbes from pet birds and encourage more research on this unexplored topic.