The increase of Lactobacillus species in the gut flora of newborn broiler chicks and ducks is associated with weight gain

Oral administration of Limosilactobacillus ingluviei C37 inhibits Campylobacter jejuni colonization in chicks

As the global population continues to grow, so too does the demand for poultry meat. However, the concurrent increase in the prevalence of drug-resistant bacteria has stimulated interest in the search for alternatives to antibiotics in poultry and livestock agriculture. One potential strategy is the use of probiotics. In this study, we showed that prophylactic oral administration of Limosilactobacillus ingluviei C37 (LIC37) reduced Campylobacter jejuni colonization of the cecum in cage-raised chicks, without causing significant changes in the overall diversity of gut bacteria. Further, the abundance of Blautia, another genus of probiotic bacteria, increased in the gastrointestinal tract following ingestion of LIC37 by chicks. These findings suggest that LIC37 could potentially be used as a novel probiotic agent against C. jejuni in livestock production.

Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population

Empirical studies from laboratory systems and humans show that the gut microbiota is linked to host health. Similar evidence for effects on traits linked to fitness in nature is rare, not least because experimentally manipulating the gut microbiota is challenging. We isolated, characterized, and cultured a bacterial strain, Lactobacillus kimchicus APC4233, directly from a wild bird (the great tit Parus major) and provided it as a self-administered dietary supplement. We assessed the impact of the treatment on the host microbiota community, on weight, and tested whether the treatment affected a previous result linking microbiota alpha diversity to weight in nestlings. The treatment dramatically increased L. kimchicus abundance in the gut microbiota and increased alpha diversity. This effect was strongest in the youngest birds, validating earlier findings pointing to a brief developmental window when the gut microbiota are most sensitive. In time-lagged models, nestling weight was higher in the treatment birds suggesting L. kimchicus may have probiotic potential. There was also a positive time-lagged relationship between diversity and weight in control birds but not in the treatment birds, suggesting L. kimchicus helped birds compensate for low alpha diversity. We discuss why ecological context is likely key when predicting impacts of the microbiome. The manipulation of the gut microbiota with a host native strain in this wild population provides direct evidence for the role of the microbiota in the ecology and evolution of natural populations.

The Catalog of Microbial Genes and Metagenome-Assembled Genomes from the Gut Microbiomes of Five Typical Crow Species on the Qinghai-Tibetan Plateau

While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai-Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows' digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds.

Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan

Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.

Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage

In the late growth stage of commercial Pekin ducks, a significant increase in feed intake and a decline in body weight gain have been observed, leading to impaired feed conversion efficiency. To address this issue, we investigated alterations in production performance, blood biochemical indices, ileum tissue architecture, and microbial community structure in Pekin ducks. The primary objective was to provide robust data supporting the improvement of meat duck production efficiency during the late growth stage (28-42-days-old). Forty 28-day-old Pekin ducks were randomly assigned to 8 replicates, with five ducks per replicate. The rearing period lasted 14 days, with feed and water provided ad libitum. Our findings indicated a significant increase in Pekin duck body and heart weights with advancing age (P < 0.05). Moreover, serum antioxidant enzyme and high-density lipoprotein concentrations significantly increased, whereas triglyceride levels decreased (P < 0.05). Notably, the height of the ileal villi was significantly reduced (P < 0.05). The microbial community structure of the ileum exhibited significant changes as ducks aged, accompanied by a substantial increase in microbial flora diversity, particularly with the formation of more tightly connected microbial network modules. Time-dependent enrichment was observed in microbial gene functions related to energy metabolism pathways. At the genus level, Sphingomonas and Subdoligranulum have emerged as crucial players in microbial differential functional pathways and network formation. These bacteria likely serve as the key driving factors in the dynamic microbial changes that occur in Pekin ducks over time. Overall, our findings suggest a potential decline in the absorption function of the small intestine and fat deposition performance of Pekin ducks during later growth stages, which may be attributed to the maturation and proliferation of the gut microbial community.

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.

Effects of probiotics on productive performances and serum lipid profile of broiler as substitute of antibiotics

OBJECTIVES

The present research was accomplished to characterize probiotics from broiler gastrointestinal tract (GIT) by profiling biochemical, antimicrobial, and antibiotic sensitivity properties. Eventually, probiotic potentiality was evaluated as a substitute for antibiotic supplements in broiler focusing growth performance, carcass characteristics, and serum lipid profile.

METHODS

Probiotic bacteria were characterized based on morphological, physiological, and several biochemical tests. Antibacterial activity against a broad spectrum of antibiotics and bacterial pathogens was detected. An in vivo trial was conducted on 40-day-old Ross 308 broiler strains during 21 days in an in vivo trial. The chicks were divided into total of five groups, a control group and four experimental groups (Antibiotic1, Antibiotic2, Probiotic1, and Probiotic2) in a completely randomized design. Probiotic was supplemented in broiler feed (2× 109 CFU/g feed) or by direct oral gavage (1× 109 CFU/chick). The variables of production performance like body weight (BW), average daily gain (ADG), feed intake (FI), and feed conversion ratio (FCR), carcass characteristics and serum lipid profile were measured.

RESULTS

10 probiotic bacteria were presumptively identified as Lactobacillus sp. based on the morphological, physiological, and strong resistance properties in several biochemical tests. The mixture of Lactobacillus had favorable effects on productive performance of broilers regarding BW, ADG, and FCR (p < .05) compared with chickens that had no additive or had antibiotic during overall period of in vivo trial. Additionally, noteworthy efficacy on carcass characteristics and serum lipid profile were found (p < .05) in Lactobacillus mixture fed chicken groups of in vivo trial.

CONCLUSION

Mixed Lactobacillus sp. can be considered as a potential additive for broiler diet attributable to noteworthy efficacy on growth performance, carcass characteristics, and serum lipid profile. Accordingly, the research highlights the need for suitable alteration of antibiotics through probiotic characterization and proper inclusion in broiler diet.

Combination of autochthonous Lactobacillus strains and trans-Cinnamaldehyde in water reduces Salmonella Heidelberg in turkey poults

Reducing the colonization of Salmonella in turkeys is critical to mitigating the risk of its contamination at later stages of production. Given the increased susceptibility of newly hatched poults to Salmonella colonization, it is crucial to implement interventions that target potential transmission routes, including drinking water. As no individual intervention explored to date is known to eliminate Salmonella, the United States Department of Agriculture-Food Safety Inspection Service (USDA-FSIS) recommends employing multiple hurdles to achieve a more meaningful reduction and minimize the potential emergence of resistance. Probiotics and plant-derived antimicrobials (PDAs) have demonstrated efficacy as interventions against Salmonella in poultry. Therefore, this study aimed to investigate the use of turkey-derived Lactobacillus probiotics (LB; a mixture of Lactobacillus salivarius UMNPBX2 and L. ingluviei UMNPBX19 isolated from turkey ileum) and a PDA, trans-cinnamaldehyde (TC), alone and in combination (CO), against S. Heidelberg in turkey drinking water and poults. The presence of 5% nutrient broth or cecal contents as contaminants in water resulted in S. Heidelberg growth. TC eliminated S. Heidelberg, regardless of the contaminants present. In contrast, the cecal contents led to increased survival of Lactobacillus in the CO group. Unlike TC, LB was most effective against S. Heidelberg when the nutrient broth was present, suggesting the role of secondary metabolites in its mechanism of action. In the experiments with poults, individual TC and LB supplementation reduced cecal S. Heidelberg in challenged poults by 1.2- and 1.7-log10 colony-forming units (CFU)/g cecal contents, respectively. Their combination yielded an additive effect, reducing S. Heidelberg by 2.7 log10 CFU/g of cecal contents compared to the control (p ≤ 0.05). However, the impact of TC and LB on the translocation of S. Heidelberg to the liver was more significant than CO. TC and LB are effective preharvest interventions against S. Heidelberg in poultry production. Nonetheless, further investigations are needed to determine the optimum application method and its efficacy in adult turkeys.

Association of Bacillus subtilis and Bacillus amyloliquefaciens: minimizes the adverse effects of necrotic enteritis in the gastrointestinal tract and improves zootechnical performance in broiler chickens

This study aimed to evaluate the efficiency and capacity of the probiotic composed of Bacillus subtilis and Bacillus amyloliquefaciens, in improving the zootechnical performance of broiler chickens challenged with Eimeria spp. and Clostridium perfringens. The broilers were distributed in a completely randomized design in poultry isolators (12 birds each), resulting in 3 treatments: T1 (control, no challenge and no Bacillus in diet), T2 (challenged with Eimeria spp., followed by Clostridium perfringens infection and no Bacillus in the diet), and T3 (challenged with Eimeria spp., Clostridium perfringens and treated with Bacillus subtilis and Bacillus amyloliquefaciens). They were evaluated for a period of 29 d, divided into preinitial (1-7 d of age), initial (8-21 d), and growth (22-29 d) phases. Assessments of body weight, weight gain, feed consumption, and feed conversion were conducted, along with the classification of the scores and optical microscopy of the tract gastrointestinal. The animals challenged and treated with the probiotic containing Bacillus spp. showed improved indicators of zootechnical performance. Additionally, the animals challenged and treated (T3) had a better score for intestinal lesions compared to the other treatment groups. Therefore, the probiotic consisting of Bacillus subtilis and Bacillus amyloliquefaciens could be considered an effective option for disease prevention and improving the zootechnical performance of broiler chickens.

Early-Life Fecal Transplantation from High Muscle Yield Rainbow Trout to Low Muscle Yield Recipients Accelerates Somatic Growth through Respiratory and Mitochondrial Efficiency Modulation

Previous studies conducted in our lab revealed microbial assemblages to vary significantly between high (ARS-FY-H) and low fillet yield (ARS-FY-L) genetic lines in adult rainbow trout. We hypothesized that a high ARS-FY-H donor microbiome can accelerate somatic growth in microbiome-depleted rainbow trout larvae of the ARS-FY-L line. Germ-depleted larvae of low ARS-FY-L line trout reared in sterile environments were exposed to high- or low-fillet yield-derived microbiomes starting at first feeding for 27 weeks. Despite weight-normalized diets, somatic mass was significantly increased in larvae receiving high fillet yield microbiome cocktails at 27 weeks post-hatch. RNA-seq from fish tails reveals enrichment in NADH dehydrogenase activity, oxygen carrier, hemoglobin complex, gas transport, and respiratory pathways in high fillet yield recolonized larvae. Transcriptome interrogation suggests a relationship between electron transport chain inputs and body weight assimilation, mediated by the gut microbiome. These findings suggest that microbiome payload originating from high fillet yield adult donors primarily accelerates juvenile somatic mass assimilation through respiratory and mitochondrial input modulation. Further microbiome studies are warranted to assess how increasing beneficial microbial taxa could be a basis for formulating appropriate pre-, pro-, or post-biotics in the form of feed additives and lead to fecal transplantation protocols for accelerated feed conversion and fillet yield in aquaculture.

Biophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks

Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.

Wild Avian Gut Microbiome at a Small Spatial Scale: A Study from a Mediterranean Island Population of Alectoris rufa

This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in-among others-habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units.

Probiotic Escherichia coli Nissle 1917 protect chicks from damage caused by Salmonella enterica serovar Enteritidis colonization

As a foodborne pathogen of global importance, Salmonella enterica serovar Enteritidis (S. Enteritidis) is a threat to public health that is mainly spread by poultry products. Intestinal Enterobacteriaceae can inhibit the colonization of S. Enteritidis and are regarded as a potential antibiotic substitute. We investigated, in chicks, the anti-S. Enteritidis effects of Escherichia coli (E. coli) Nissle 1917, the most well-known probiotic member of Enterobacteriaceae. Eighty 1-d-old healthy female AA broilers were randomly divided into 4 groups, with 20 in each group, namely the negative control (group P), the E. coli Nissle 1917-treated group (group N), the S. Enteritidis-infected group (group S) and the E. coli Nissle 1917-treated and S. Enteritidis-infected group (group NS). From d 5 to 7, chicks in groups N and NS were orally gavaged once a day with E. coli Nissle 1917 and in groups P and S were administered the same volume of sterile PBS. At d 8, the chicks in groups S and NS were orally gavaged with S. Enteritidis and in groups P and N were administered the same volume of sterile PBS. Sampling was conducted 24 h after challenge. Results showed that gavage of E. coli Nissle 1917 reduced the spleen index, Salmonella loads, and inflammation (P < 0.05). It improved intestinal morphology and intestinal barrier function (P < 0.05). S. Enteritidis infection significantly reduced mRNA expression of angiotensin-converting enzyme 2 (ACE2) and solute carrier family 6-member 19 (SLC6A19) in the cecum and the content of Gly, Ser, Gln, and Trp in the serum (P < 0.05). Pretreatment with E. coli Nissle 1917 yielded mRNA expression of ACE2 and SLC6A19 in the cecum and levels of Gly, Ser, Gln, and Trp in the serum similar to that of uninfected chicks (P < 0.05). Additionally, E. coli Nissle 1917 altered cecum microbiota composition and enriched the abundance of E. coli, Lactobacillales, and Lachnospiraceae. These findings reveal that the probiotic E. coli Nissle 1917 reduced S. Enteritidis infection and shows enormous potential as an alternative to antibiotics.

In vitro fermentation properties of magnesium hydride and related modulation effects on broiler cecal microbiome and metabolome

Magnesium hydride (MGH), a highly promising hydrogen-producing substance/additive for hydrogen production through its hydrolysis reaction, has the potential to enhance broiler production. However, before incorporating MGH as a hydrogen-producing additive in broiler feed, it is crucial to fully understand its impact on microbiota and metabolites. In vitro fermentation models provide a fast, reproducible, and direct assessment tool for microbiota metabolism and composition. This study aims to investigate the effects of MGH and coated-magnesium hydride (CMG) on fermentation characteristics, as well as the microbiota and metabolome in the culture of in vitro fermentation using cecal inocula from broilers. After 48 h of incubation, it was observed that the presence of MGH had a significant impact on various factors. Specifically, the content of N-NH3 decreased, while the total hydrogen gas and total SCFAs increased. Furthermore, the presence of MGH promoted the abundance of SCFA-producing bacteria such as Ruminococcus, Blautia, Coprobacillus, and Dysgonomonas. On the other hand, the presence of CMG led to an increase in the concentration of lactic acid, acetic acid, and valeric acid. Additionally, CMG affected the diversity of microbiota in the culture, resulting in an enrichment of the relative abundance of Firmicutes, as well as genera of Lactobacillus, Coprococcus, and Eubacterium. Conversely, the relative abundance of the phylum Proteobacteria and pathogenic bacteria Shigella decreased. Metabolome analysis revealed that MGH and CMG treatment caused significant changes in 21 co-regulated metabolites, primarily associated with lipid, amino acid, benzenoids, and organooxygen compounds. Importantly, joint correlation analysis revealed that MGH or CMG treatments had a direct impact on the microbiota, which in turn indirectly influenced metabolites in the culture. In summary, the results of this study suggested that both MGH and coated-MGH have similar yet distinct positive effects on the microbiota and metabolites of the broiler cecal in an in vitro fermentation model.

Limosilactobacillus fermentum, Lactococcus lactis and Thomasclavelia ramosa are enriched and Methanobrevibacter smithii is depleted in patients with non-alcoholic steatohepatitis

Non-alcoholic fatty liver (NAFLD), and its complicated form, non-alcoholic steatohepatitis (NASH), have been associated with gut dysbiosis with specific signatures. Endogenous ethanol production by Klebsiella pneumoniae or yeasts has been identified as a potential physio-pathological mechanism. A species-specific association between Lactobacillus and obesity and metabolic diseases has been reported. In this study, the microbial composition of ten cases of NASH and ten controls was determined using v3v4 16S amplicon sequencing as well as quantitative PCR (qPCR). Using different statistical approaches, we found an association of Lactobacillus and Lactoccocus with NASH, and an association of Methanobrevibacter, Faecalibacterium and Romboutsia with controls. At the species level, Limosilactobacillus fermentum and Lactococcus lactis, two species producing ethanol, and Thomasclavelia ramosa, a species already associated with dysbiosis, were associated with NASH. Using qPCR, we observed a decreased frequency of Methanobrevibacter smithii and confirmed the high prevalence of L. fermentum in NASH samples (5/10), while all control samples were negative (p = 0.02). In contrast, Ligilactobacillus ruminis was associated with controls. This supports the critical importance of taxonomic resolution at the species level, notably with the recent taxonomic reclassification of the Lactobacillus genus. Our results point towards the potential instrumental role of ethanol-producing gut microbes in NASH patients, notably lactic acid bacteria, opening new avenues for prevention and treatment.

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

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

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens

The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

Differences in intestinal microflora of birds among different ecological types

The intestinal microflora of animals plays a key role in metabolism, immunity, and development. Birds distributed across multiple ecological habitats. However, little is known about the differences in the intestinal microflora of birds among different ecological types. In this study, bird feces from different ecological types and orders were collected in Chongqing Zoo, China. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function differences of gut microbiota communities among different ecological types/orders. Firmicutes and Proteobacteria were the dominant bacteria phyla for all samples but there were significant differences in the α-diversity, community structure and microbial interactions between birds of different ecological types. The function differences involve most aspects of the body functions, especially for environmental information processing, organismal systems, human diseases, genetic information processing, and metabolism. These results suggest that diet and habitat are potential drivers of avian gut microbial aggregation. This preliminary study is of great significance for further research on the intestinal microflora of different ecological types of birds.

Microbial communities in developmental stages of lucinid bivalves

Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.

Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens

Moult is a normal physiological phenomenon in poultry. Induced molting (IM) is the most widely used and economical molting technique. By inducing moult, the laying hens can grow new feathers during the next laying cycle and improve laying performance. However, the lack of energy supply has a huge impact on both the liver and intestines and acts on the intestines and liver through the “gut-liver axis”. More importantly, lipid metabolism in the liver is closely related to the laying performance of laying hens. Therefore, in this study, cecal metabolites and liver transcriptome data during IM of laying hens at the late stage of laying (stop feeding method) were analyzed together to reveal the regulatory mechanism of “gut-liver axis” affecting the laying performance of laying hens from the perspective of lipid metabolism. Transcriptome analysis revealed that 4,796 genes were obtained, among which 2,784 genes had significant differences (p < 0.05). Forty-nine genes were associated with lipid metabolism, and five core genes (AGPAT2, SGPL1, SPTLC1, PISD, and CYP51A1) were identified by WGCNA. Most of these differential genes are enriched in steroid biosynthesis, cholesterol metabolism, drug metabolism—cytochrome P450, synthesis and degradation of ketone bodies, PPAR signaling pathway, and bile secretion. A total of 96 differential metabolites were obtained by correlating them with metabolome data. Induced moult affects laying performance by regulating genes related to lipid metabolism, and the cecal metabolites associated with these genes are likely to regulate the expression of these genes through the “enterohepatic circulation”. This experiment enriched the theoretical basis of induced moult and provided the basis for prolonging the feeding cycle of laying hens.

Increase Dietary Fiber Intake Ameliorates Cecal Morphology and Drives Cecal Species-Specific of Short-Chain Fatty Acids in White Pekin Ducks

The current study was to investigate the modulatory effects of total dietary fiber (TDF) levels on cecal morphology and the response of microbiota to maintain gut health for duck growth. A total of 192 14-day-old male white Pekin ducks were randomly allocated to three dietary groups and fed diets, containing 12.4, 14.7, and 16.2% TDF, respectively, until 35 days under the quantitative feed intake. Each dietary group consisted of eight replicate cages of eight birds. The results revealed that 14.7 and 16.2% TDF groups significantly promoted growth performance and improved villus height, the ratio of villus to crypt, muscle layer thickness, and goblet cells per villus of cecum in ducks. qPCR results showed that the transcriptional expression of Claudin-1, Muc2, IGF-1, and SLC16A1 was significantly upregulated in cecum in 14.7 and 16.2% TDF groups. Meanwhile, the concentration of IGF-1 in circulating was significantly increased in 14.7 and 16.2% TDF groups while that of DAO was significantly decreased in 16.2% TDF group. Furthermore, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum were conspicuously improved in 14.7 and 16.2% TDF groups while that of propionate was significantly decreased. In addition, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum presented negative correlations with the concentration of DAO in circulating. 16S rRNA gene sequencing results showed that the 14.7% TDF group importantly elevated the microbial richness. Simultaneously, butyrate-producing bacteria like the family Lachnospiraceae, Oscillospiraceae, and Erysipelatoclostridiaceae were enriched as biomarkers in the 16.2% TDF group. Correlation network analysis revealed that the associations between specific bacteria and short-chain fatty acids (SCFAs) induced by different TDF levels, and the correlations among bacteria were also witnessed. For example, the genus Monoglobus and CHKCI002 showed a positive correlation with butyrate, and there was a positively coexistent association between Monoglobus and CHKCI002. In summary, these data revealed that increasing the TDF level could enhance the cecal morphology and drive cecal species-specific of SCFAs in ducks.

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

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

Effects of Coated Sodium Butyrate and Polysaccharides From Cordyceps cicadae on Intestinal Tissue Morphology and Ileal Microbiome of Squabs

This experiment was conducted to investigate the effects of dietary supplementation with different levels of coated sodium butyrate (CSB) and polysaccharides extracted from Cordyceps cicadae (CCP) on growth performance, intestinal tissue morphology and ileum microbiome in squabs. A total of 420 1-day-old squabs were randomly divided into seven groups with 5 replicates each and 12 squabs per replicate. The squabs were fed basal diet (control group) and basal diet supplemented with different levels of CSB (275, 550, and 1,100 mg/kg, groups CSB-275, CSB-550, CSB-1100) and CCP (27.5, 55, and 110 mg/kg, groups CCP-27.5, CCP-55, and CCP-110), respectively. The experiment was conducted for 28 days. The results revealed that the final BW and average daily gain concentration were higher (P < 0.05) in squabs of CSB-275 and CCP-110 groups than those in the CON group. Comparing with control group, the squabs in the groups CSB-275, CSB-550, and CCP-55 obtained higher villus height/crypt depth (VH/CD) of the duodenum and higher VH of the jejunum (P < 0.05). Operational taxonomic units in the groups CSB-550 and CCP-27.5 were also increased (P < 0.05). Regarding the relative abundance of flora, the Actinobacteria abundance in the groups CSB-550, CSB-1100, and CCP-55 were higher than in control group (P < 0.05), and the Aeriscardovia abundance of CSB-275, CSB-550, CSB-1100, and CCP-110 were elevated (P < 0.05). However, the Enterococcus abundance in CSB-275, CSB-550, CSB-1100, and CCP-27.5 decreased (P < 0.05). In summary, results obtained in the present study indicate that CSB and CCP can improve growth performance, intestinal microbial balance and gut health of squabs.

Effects of Compound Probiotics on Cecal Microbiome and Metabolome of Shaoxing Duck

This experiment was conducted to investigate the effects of compound probiotics on intestinal microflora and metabolome of Shaoxing ducks. A total of 640 1-day-old Shaoxing ducks were randomly divided into two treatments with eight replicates and forty ducks for each replicate. The ducks were fed basal diet (Ctrl) and basal diet supplemented with 0.15% compound probiotics (MixP). The experiment lasted for 85 days. The results showed that the abundance of Bacteroidetes and Bacteroides in MixP was higher than that in Ctrl (P < 0.05). However, the abundance of Firmicutes and Oscillospira and Desulfovibrio in MixP was lower than that in Ctrl (P < 0.05). Concentrations of 71 metabolites differed significantly (P < 0.05) between the MixP and the Ctrl groups; for example, Pyridoxal (Vitamin B6), L-Arginine, and Betaine aldehyde were up-regulated (P < 0.05), and 7-oxocholesterol, 3-hydroxy-L-kynureni-ne, and N-acetyl-d-glucosamine were down-regulated (P < 0.05). KEGG was enriched in 15 metabolic pathways. The pathways of Vitamin B6 metabolism, Vascular smooth muscle contraction, Vitamin digestion and absorption, and Protein digestion and absorption were influenced by compound probiotics supplementation. Thus, supplementation of compound probiotics improved cecal heath through shifts in the cecal microbiome and metabolome.

Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird

Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.

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

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

Effects of Enterococcus faecalis administration on the community structure of airborne bacteria in weanling piglet and layer hen houses

Probiotics have been shown to improve microbial compositions in animal intestine and feces, but the effects of probiotic administration on airborne microbial composition in animal houses remain unclear. In this study, we investigated the effects of dietary Enterococcus faecalis on the bacterial community structure in the air of piglet and layer hen houses. Indoor air and feces from piglet and layer hen houses were sampled after supplementing E. faecalis in feed for 60 days, and bacterial community structures were analyzed using Illumina high-throughput sequencing technology. Results showed that Chao1, ACE, Shannon, and Simpson indices of bacterial diversity did not significantly change in feces or indoor air of piglet or layer hen after supplementation with E. faecalis (P > 0.05). However, E. faecalis administration resulted in a decrease in the relative abundance of Proteobacteria (P < 0.05). In addition, E. faecalis significantly reduced the relative abundance of opportunistic pathogens such as Acinetobacter, Escherichia, and Shigella (P < 0.05), and beneficial bacterial genus such as Lactobacillus was significantly enriched in both feces and indoor air (P < 0.05). These changes should be of benefit to livestock, farm workers, and the surrounding environment.

Gut Microbiota Dynamics, Growth Performance, and Gut Morphology in Broiler Chickens Fed Diets Varying in Energy Density with or without Bacitracin Methylene Disalicylate (BMD)

High-energy-density diet could increase body weight at the expense of the intestinal health of the animals. In order to optimize production without negatively influencing the gut health of chickens, dietary supplementation with bacitracin methylene disalicylate (BMD) is a common feeding strategy adopted to enhance production performance and intestinal health. Studies have suggested that BMD could improve chicken growth performance and gut health through modulation of the gut microbiota. The current study investigated the effect of BMD supplementation in a normal-energy (NE) or high-energy (HE) diet on growth performance, organ weights, jejunal morphology, and gut microbiota of broiler chickens at different growth stages. Birds were allocated to four treatments: normal-energy basal diet (NE-BAS), normal-energy BMD diet (NE-BMD), high-energy basal diet (HE-BAS), and high-energy BMD diet (HE-BMD). In the starter phase, body weight and body weight gain were reduced significantly (p < 0.05) in chickens fed HE diets compared to those fed NE diets. The FCR was significantly higher (p < 0.05) in birds fed HE-BMD diets in the starter phase but lower (p < 0.05) during the grower phase when compared to other treatments. Moreover, the relative bursa weight increased significantly (p = 0.0220) among birds that received HE diets. Birds fed HE-BMD had greater villus height (p = 0.054) than NE-BMD group. Among the chickens fed the HE diets, those that received BMD treatment had a significantly increased (p = 0.003) villus width (13.3% increase) compared to those that received the basal diet. Improved population of Firmicutes was observed in chickens fed HE-BMD diet when compared to HE-BAS. Our results imply that BMD may be more effective in improving intestinal health when supplemented in a high-energy diet for broiler chickens.

Dietary purslane (Portulaca oleracea L.) promotes the growth performance of broilers by modulation of gut microbiota

Purslane is a widespread wild vegetable with both medicinal and edible properties. It is highly appreciated for its high nutritional value and is also considered as a high-quality feed resource for livestock and poultry. In this study, Sanhuang broilers were used to investigate the effect of feeding purslane diets on the growth performance in broilers and their gut microbiota. A total of 48 birds with good growth and uniform weight were selected and randomly allocated to four treatment groups A (control), B, C and D. Dietary treatments were fed with basal diet without purslane and diets containing 1%, 2% and 3% purslane. The 16S rDNA was amplified by PCR and sequenced using the Illumina HiSeq platform to analyze the composition and diversity of gut microbiota in the four sets of samples. The results showed that dietary inclusion of 2% and 3% purslane could significantly improve the growth performance and reduce the feed conversion ratio. Microbial diversity analysis indicated that the composition of gut microbiota of Sanhuang broilers mainly included Gallibacterium, Bacteroides and Escherichia-Shigella, etc. As the content of purslane was increased, the abundance of Lactobacillus increased significantly, and Escherichia-Shigella decreased. LEfSe analysis revealed that Bacteroides_caecigallinarum, Lachnospiraceae, Lactobacillales and Firmicutes had significant differences compared with the control group. PICRUSt analysis revealed bacteria mainly enriched in carbohydrate metabolism pathway due to the additon of purslane in the diet. These results suggest that the addition of purslane to feed could increase the abundance of Lactobacillus in intestine, modulate the environment of gut microbiota and promote the metabolism of carbohydrates to improve its growth performance. This study indicates that the effect of purslane on the growth-promoting performance of broilers might depend on its modulation on gut microbiota, so as to provide a certain scientific basis for the application of purslane in the feed industry.

A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits

Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore juvenile viability may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits. We collected data on two traits associated with fitness in wild nestling great tits Parus major: weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at Day-8 (D8) and Day-15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not. There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship where weight at D15 was negatively associated with the microbial diversity at D8, controlling for weight at D8, therefore reflecting relative weight gain over the intervening period. Indicator species analysis revealed that specificity values were high and fidelity values were low, suggesting that indicator taxa were primarily detected within either the survived or not survived groups, but not always detected in birds that either survived or died. Therefore these indicator taxa may be sufficient, but not necessary for determining either survival or mortality, perhaps owing to functional overlap in microbiota. We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects may be best investigated longitudinally to detect critical development windows for key microbiota and host traits associated with neonatal weight. Our findings should inform future hypothesis testing to pinpoint which features of the gut microbial community impact on host fitness, and when during development this occurs. Such confirmatory research will shed light on population level processes and could have the potential to support conservation.

Changes of the mice intestinal microbes by the oligosaccharides-enriched fermented milk in a gender-dependent pattern

Oligosaccharides are prebiotics that can be used to regulate microbes in the host intestine. In this study, we investigated the effects of different oligosaccharides on the changes of the intestinal microbial communities and co-related functional genes in the intestinal microbes. Fructo-oligosaccharide (FOS), galacto-oligosaccharide (GOS) and oligomannose (MOS) were enriched in milk and fermented by Lactobacillus plantarum and tested in ICR mice model in vivo. Then the changes of the fecal microbial communities were examined by 16S rDNA gene sequencing approach. We found that the relative abundance of several taxa was markedly different between genders at the level of phylum and genera, additionally to the changes in the microbial community. Meanwhile, compared with male mice, the intestinal microbes of the female mice group had significant changes. Furthermore, the intestinal microbial diversity was enhanced in the female mice when treated with the FOS enriched fermented milk. Therefore, this data suggests that oligosaccharides have the potential to improve the host microbial diversity in the intestinal tract, and FOS has potential applications in the fermented dairy industry. It revealed a gender-dependent changes of different oligosaccharides-enriched fermented milk on the intestinal microbes of mice, providing a reference for regulating the intestinal microbes by oligosaccharides.

Comparative Analysis of the Gut Microbial Communities of the Eurasian Kestrel (Falco tinnunculus) at Different Developmental Stages

The gut microflora play a very important role in the life of animals. Although an increasing number of studies have investigated the gut microbiota of birds in recent years, there is a lack of research work on the gut microbiota of wild birds, especially carnivorous raptors, which are thought to be pathogen vectors. There are also a lack of studies focused on the dynamics of the gut microbiota during development in raptors. In this study, 16S rRNA gene amplicon high-throughput sequencing was used to analyze the gut microbiota community composition of a medium-sized raptor, the Eurasian Kestrel (Falco tinnunculus), and to reveal stage-specific signatures in the gut microbiota of nestlings during the pre-fledging period. Moreover, differences in the gut microbiota between adults and nestlings in the same habitat were explored. The results indicated that the Eurasian Kestrel hosts a diverse assemblage of gut microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the primary phyla shared within the guts of adults and chicks. However, adults harbored higher abundances of Proteobacteria while nestlings exhibited higher abundances of Firmicutes and Actinobacteria, and consequently the majority of dominant genera observed in chicks differed from those in adults. Although no significant differences in diversity were observed across the age groups during nestling ontogeny, chicks from all growth stages harbored richer and more diverse bacterial communities than adults. In contrast, the differences in gut microbial communities between adults and younger nestlings were more pronounced. The gut microbes of the nestlings in the last growth stage were converged with those of the adults. This study provides basic reference data for investigations of the gut microbiota community structure of wild birds and deepens our understanding of the dynamics of the gut microflora during raptor development.

Light at night affects gut microbial community and negatively impacts host physiology in diurnal animals: Evidence from captive zebra finches

The gastrointestinal tract (GIT) hosts a large number of diverse microorganisms, with mutualistic interactions with the host. Here, in two separate experiments, we investigated whether light at night (LAN) would affect GIT microbiota and, in turn, the host physiology in diurnal zebra finches (Taeniopygia guttata). Experiment I assessed the effects of no-night (LL) and dimly illuminated night (dim light at night, dLAN) on fecal microbiota diversity and host physiology of birds born and raised under 12 h photoperiod (LD; 12 h light: 12 h darkness). Under LL and dLAN, compared to LD, we found a significant increase in the body mass, subcutaneous fat deposition and hepatic accumulation of lipids. Although we found no difference in total 24 h food consumption, LL/ dLAN birds ate also at night, suggesting LAN-induced alteration in daily feeding times. Concurrently, there were marked differences in amplicon sequence and bacterial species richness between LD and LAN, with notable decline in Lactobacillus richness in birds under LL and dLAN. We attributed declined Lactobacillus population as causal (at least partially) to negative effects on the host metabolism. Therefore, in experiment II with similar protocol, birds under LL and dLAN were fed on diet with or without Lactobacillus rhamnosus GG (LGG) supplement. Clearly, LGG supplement ameliorated LL- and dLAN-induced negative effects in zebra finches. These results demonstrate adverse effects of unnatural lighting on GIT bacterial diversity and host physiology, and suggest the role of GIT microbiota in the maintenance of metabolic homeostasis in response to LAN environment in diurnal animals.

Lactobacillus ingluviei C37 from chicken inhibits inflammation in LPS-stimulated mouse macrophages

Probiotics are growing alternatives to antibiotics, and can contribute to the prevention and treatment of diseases and enhance livestock production. Lactobacillus (L.) ingluviei is a novel probiotic species with growth-enhancement effects; however, this species remains poorly understood, and there have been (to our knowledge) no studies focusing on its immunological effects. Here, we isolated L. ingluviei C37 (LIC37) from chicken and evaluated the bacterium's immunomodulatory properties to explore its probiotic potential. Real-time quantitative PCR and ELISA showed that in vitro exposure of inflammation-stimulated mouse peritoneal macrophages to heat-killed LIC37 led to decreases in tumor necrosis factor-α and interleukin (IL)-6 levels and an increase in IL-10. These findings suggested that LIC37 exerts anti-inflammatory effects by modulating cytokine profiles. This species may be an attractive probiotic bacterial strain for use in animal production.

Probiotic bacteria maintain normal growth mechanisms of heat stressed broiler chickens

Probiotics have growth promoting effects even under periods of heat stress challenge. More information is needed to understand the mechanisms by which probiotics maintain the growth performance. The aim of this study was to evaluate the effect of a probiotic based on Bacillus subtilis bacteria on growth related mechanisms of broilers under heat stress conditions. Specifically, growth performance, skeletal bone characteristics, skeletal muscles size, intestinal villus-crypt structure, intestinal bacteria, growth hormone (GH), insulin-like growth factor-1 (IGF-1), cholesterol, and glucose. A total of 1200 one day old Ross 308 male broilers were randomly distributed into 4 treatments, with 12 replicates per treatment and 25 birds per replicate. A 2 × 2 factorial arrangement was used; the main factors were environmental temperature (thermoneutral or heat stress) and diet (control or control + B. subtilis; 3 × 10⁷ cfu/kg of feed). From d 22 to 35 of age, birds were either exposed to thermoneutral conditions (21 °C) or chronic heat stress (30 °C). During the same period, each group was divided into 2 subgroups and fed either the control diet or the B. subtilis supplemented diet. The results demonstrated that B. subtilis had positive effects (P < 0.05) on the body weight gain, feed conversion ratio, villus height, crypt depth, villus surface area, absorptive epithelial cell area and viable counts of intestinal beneficial bacteria. B. subtilis increased (P < 0.05) serum GH, IGF-1 and maintain normal levels of cholesterol and glucose under heat stress conditions. In addition, broilers fed B. subtilis under heat stress conditions exhibited higher (P < 0.05) skeletal muscles size and improved (P < 0.05) tibia traits and lower (P < 0.05) abdominal fat pads deposition compared with the controls. B. subtilis had no effect on rectal temperature under thermoneutral or heat stress conditions. It is concluded that B. subtilis can be used as growth promoters in broilers, particularly during the periods of heat stress conditions.

Bamboo leaf flavone changed the community of cecum microbiota and improved the immune function in broilers

It has been shown that bamboo leaf flavone (BLF) displays biological and pharmacological activities in mammals. However, the effects of BLF on broiler gut microbiota and related immune function have not been investigated. The aim of this study was to test our hypothesis that BLF can improve the health status of broilers by modulating the gut microbiota. A total of 300 one-day-old Arbor Acres (AA) broilers were used to characterize their gut microbiota and immune status after feeding diet supplemented with BLF. The V4 hypervariable region of the 16S rRNA gene from cecal bacteria was sequenced via the Illumina MiSeq platform. The Immune status and related parameters were assessed, including the immune organ index (the spleen, thymus, and bursa), serum concentrations of IL-2 and INF-γ, and spleen IL-2 and INF-γ gene expressions. The results showed the BLF diet had an Immune enhancement effect on broilers. In addition, BFL caused the changes of the gut microbial community structure, resulting in greater proportions of bacterial taxa belonging to Lactobacillus, Clostridiales, Ruminococcus, and Lachnospiraceae. These bacteria have been used as probiotics for producing short chain fatty acids in hosts. These results indicate that BLF supplement improves immune function in chicken via modulation of the gut microbiota.

Isolation and preliminary screening of potentially probiotic Weissella confusa strains from healthy human feces by culturomics

PURPOSE

The objective of this study was to isolate and identify strains of bacteria from feces of healthy human and screen potential probiotic candidate by using culturomics method combined with the matrix-assisted laser desorption/ionization-time of flight mass spectrum (MALDI-TOF MS) and 16S rRNA gene sequencing.

METHODS AND RESULTS

31 strains were isolated and purified from human feces by culturomics method, and identified by MALDI-TOF MS and 16S rRNA gene sequencing. Then the obtained strains were tested for haemolytic activity, antibiotic susceptibility, acid and bile salts tolerance, antimicrobial activity, morphological and physiological characteristics. Three potential probiotic candidate strains named YM5Y, YM5S1 and YM5S2 were selected and identified as Weissella confusa.

CONCLUSION

Our results suggest the culturomics approach could be used to isolate and screen human fecal strains which could eventually be used for the development of novel probiotics. In addition, the isolated strains of W. confusa can act as potential probiotics and should be explored further for their potential application.

Paternal weight of ducks may have an influence on offspring' small intestinal function and cecal microorganisms

Background

In animals, many factors affect the small intestinal function and cecal microorganisms, including body weight and genetic background. However, whether paternal weight impacts the small intestinal function and cecal microorganisms remains unknown to date. The current study used Nonghua sheldrake to estimate the effect of paternal weight on the intestine of the offspring by evaluating differences in small intestinal morphology, digestive enzyme activity, and cecal microorganisms between the offspring of male parents with high body weight (group H) and that of male parents with low body weight (group L).

Results

The results of the analysis of small intestinal morphology showed that the villus height of the jejunum of group H ducks was higher than that of group L ducks, and the difference was significant for ducks at 10 weeks of age. Moreover, the villus height/crypt depth of the duodenum in group H significantly exceeded that of group L at a duck age of 2 weeks. The amylase activity in the jejunum content of group H exceeded that of group L at 5 and 10 weeks of age. Furthermore, the proportion of the Firmicutes to Bacteroidetes was significantly higher in group H (duck age of 2 weeks). Among the genera with a relative abundance exceeding 1%, the relative abundances of genera Desulfovibrio, Megamonas, Alistipes, Faecalibacterium, and Streptococcus observed in group H were significantly different between group H and group L.

Conclusions

For the first time, this study identifies the effect of paternal weight on offspring small intestinal function and cecal microorganisms. Consequently, this lays a foundation for further research on the relationship between male parents and offspring intestinal function.

Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics

Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.

Effects of dietary inulin supplementation on the composition and dynamics of cecal microbiota and growth-related parameters in broiler chickens

Inulin, a prebiotic, is an attractive alternative to antibiotic growth promoters in chickens. Dietary supplementation with inulin can improve growth performance, carcass yield, immune system activity, and serum biochemical parameters in chickens. A few studies investigated the impact of dietary inulin supplementation on chicken intestinal microbiota. In this study, we investigated how and why dietary supplementation with 1, 2, and 4% inulin can affect body weight gain, feed intake, food conversion rate, immunological parameters, serum biochemical parameters, and composition and dynamics of the cecal microbiota of Tegel broiler chickens using quantitative fluorescence in situ hybridization (qFISH). We showed that inulin inclusion has a negative effect on growth performance parameters before day 21 and a positive effect subsequently up to day 42. Quantitative FISH data revealed an age-dependent change in the cecal microbiota in the control broilers fed no inulin. Thus, relative abundances of Firmicutes and Actinobacteria decreased from 52.8 to 48.3% of total cells and from 8.7 to 1.4% at days 7 and 42, respectively. However, relative abundances of Bacteroidetes and Proteobacteria gradually increased from 9.3 to 26.9% of the total cells and from 10.7 to 21.1%, respectively, over the same periods. Inulin inclusion appeared to lower the relative abundances of Lactobacillus johnsonii and Bifidobacterium species at an early bird age, but it subsequently significantly (P < 0.05) increased their relative abundances. Such increases positively correlated with body weight gain of the birds, determined after day 21. Thus, dietary supplementation with inulin together with the addition of L. johnsonii and Bifidobacterium (B. gallinarum and B. pullorum) cultures at an early age may help overcome its early negative influence on growth performance. We believe that these findings can improve our knowledge on how inulin can change the intestinal microbiota of broiler chickens and help in developing an inulin feeding regime to optimize its beneficial role in chicken development.

A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes

In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal. Therefore, we tested for phylosymbiosis among all 15 species of cranes (family Gruidae) housed in the same captive environment and maintained on identical diets. 16S rRNA sequencing revealed that crane species harbour distinct gut microbiota. Overall, we detected marginally significant patterns of phylosymbiosis, the strength of which was increased when including the estimates of absolute microbial abundance (rather than relative abundance) derived from microbial densities determined by flow cytometry. Using this approach, we detected the statistically significant signatures of phylosymbiosis only after removing male cranes from our analysis, suggesting that using mixed-sex animal cohorts may prevent the detection of phylosymbiosis. Though weak compared with mammals (and especially insects), these results provide evidence of phylosymbiosis in birds. We discuss the potential differences between birds and mammals, such as transmission routes and host filtering, that may underlie the differences in the strength of phylosymbiosis.

Association between Bioactive Molecules in Breast Milk and Type 1 Diabetes Mellitus

The association between breastfeeding and type 1 diabetes mellitus (T1DM) is controversial. However, several recent studies have established a link between these two factors, necessitating a need to review this subject to raise public awareness. Current research indicates that breast milk contains a variety of bioactive substances including immunoglobulins, oligosaccharides, insulin, lactoferrin, lysozyme, cytokines, epidermal growth factors, leukocytes, nucleotides, beneficial bacteria and vitamins. Such substances strengthen the breastfeeding infant's immune system, both directly, by increasing gut microbiota diversity and attacking harmful bacteria and pro-inflammatory molecules, and indirectly, by increasing thymus performance. Accordingly, a lack of or inadequate breastfeeding may predispose infants to several autoimmune disorders, including T1DM. Nursing mothers and caregivers are therefore advised to follow optimal breastfeeding practices prior to introducing complementary foods.

Effects of probiotics on cecal microbiome profile altered by duck Escherichia coli 17 infection in Cherry Valley ducks

Avian colibacillosis is one of the most serious infectious bacterial diseases that endanger the modern poultry industry. Lactobacillus is believed to inhibit intestinal pathogens and maintain a healthy gut microbiota. This study aimed to investigate Lactobacillus supplementation in Cherry Valley ducks to prevent the intestinal flora dysbiosis caused by Duck Escherichia coli 17. One hundred and twenty healthy one day old Cherry Valley ducks were randomized to three study groups (Group I = the control group; Group II = duck Escherichia coli 17 challenge group and Group III = DE17 challenge group supplemented with lactic acid bacteria composite preparation). Cherry Valley ducks in Group II and Group III were gavage challenged with DE17 (1 × 10⁵ CFU/mL) on day 14. Pyrosequencing of the V3/V4 variable regions of the genes encoding for 16S rRNA was used for sequence analysis. The results showed that the normal intestinal microecology was affected by DE17, including a relative increase in proteobacteria. At the same time, the Lactobacillales were increased and harmful bacteria were decreased in different intestinal segments of ducks in Group III, compared to those in Group II. Network analysis showed that dietary lactic acid bacteria addition improved the interaction pattern within the cecal microbiota of ducks and the result showed that in Ruminococcus_2 was independently present in the group III and Lachnospiraceae_NK4A136_group species correlation existed between group I and group III. This study proved that oral supplementation with Lactobacillus casei 1.2435, Lactobacillus rhamnosus 621 and Lactobacillus rhamnosus A4 can mitigate DE17 induced intestinal flora dysbiosis.

Effect of oral spray with Lactobacillus on growth performance, intestinal development and microflora population of ducklings

OBJECTIVE

The aim of this study is to investigate the effect of oral spray with probiotics on the intestinal development and microflora colonization of hatched ducklings.

METHODS

In Exp. 1, an one-way factorial design was used to study the antibacterial activity of the probiotics and metabolites on Escherichia coli (E. coli) without antimicrobial resistance. There were four experimental groups including saline as control and Lactobacillus, Bacillus subtilis, combined Lactobacillus and Bacillus subtilis groups. In Exp. 2, 64-day-old ducklings were allotted to 2 treatments with 4 replicated pens. Birds in the control group were fed a basal diet supplemented with Lactobacillus fermentation in the feed whereas birds in the oral spray group were fed the basal diet and administrated Lactobacillus fermentation by oral spray way during the first week.

RESULTS

In Exp. 1, the antibacterial activities of probiotics and metabolites on E. coli were determined by the diameter of inhibition zone in order: Lactobacillus>combined Lactobacillusand Bacillus subtilis>Bacillus subtilis. Additionally, compared to E. coli without resistance, E. coli with resistance showed a smaller diameter of inhibition zones. In Exp. 2, compared to control feeding group, oral spray group increased (p<0.05) the final body weight at d 21 and average daily gain for d 1-21 and the absolute weight of the jejunum, ileum and total intestine tract as well as cecum Lactobacillus amount at d 21.

CONCLUSION

Lactobacillus exhibited a lower antibacterial activity on E. coli with resistance than E. coli without resistance. Oral spray with Lactobacillus fermentation during the first week of could improve the intestinal development, morphological structure, and microbial balance to promote growth performance of ducklings from hatch to 21 d of age.

Review article: can bugs be drugs? The potential of probiotics and prebiotics as treatment for non-alcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) has become the most common chronic liver condition. A major current research effort is ongoing to find potential strategies to treat NAFLD-non-alcoholic steatohepatitis (NASH), with special attention to the gut microbiota. Multiple animal studies and pilot clinical trials are assessing different gut microbiota modulating strategies such as faecal microbiota transplantation, antibiotics, probiotics, prebiotics and synbiotics.

AIM

To review the role of microbiota in NAFLD-NASH and determine whether pro- and prebiotics have potential as treatment METHODS: Information was obtained from critically reviewing literature on PubMed on targeting the gut microbiota in NAFLD. Search terms included NAFLD, NASH, non-alcoholic fatty liver disease, steatohepatitis; combined with microbiome, microbiota, gut bacteria, probiotics and prebiotics.

RESULTS

Animal studies and the first emerging studies in humans show promising results for both the common probiotics Lactobacillus, Bifidobacterium and Streptococci as for short chain fatty acid (SCFA) butyrate-producing bacteria. Also, prebiotics have positive effects on different mechanisms underlying NAFLD-NASH.

CONCLUSIONS

The most promising strategies thus far developed to alter the microbiome in NAFLD-NASH are probiotics and prebiotics. However, pre- and probiotic treatment of NAFLD-NASH is relatively new and still under development. Actual understanding of the involved mechanisms is lacking and changes in the intestinal microbiota composition after treatment are rarely measured. Furthermore, large clinical trials with comparative endpoints are unavailable. Personalised treatment based on metagenomics gut microbiota analysis will probably be part of the future diagnosis and treatment of NAFLD-NASH.

Analysis of excreta bacterial community after forced molting in aged laying hens

Objective

As laying hens become aged, laying performance and egg quality are generally impaired. One of the practical methods to rejuvenate production and egg quality of aged laying hens with decreasing productivity is a forced molting. However, the changes in intestinal microbiota after forced molting of aged hens are not clearly known. The aim of the present study was to analyze the changes in excreta bacterial communities after forced molting of aged laying hens.

Methods

A total of one hundred 66-wk-old Hy-Line Brown laying hens were induced to molt by a 2-d water removal and an 11-d fasting until egg production completely ceased. The excreta samples of 16 hens with similar body weight were collected before and immediately after molting. Excreta bacterial communities were analyzed by high-throughput sequencing of bacterial 16S rRNA genes.

Results

Bacteroidetes, Firmicutes, and Proteobacteria were the three major bacterial phyla in pre-molting and immediate post-molting hens, accounting for more than 98.0%. Lactobacillus genus had relatively high abundance in both group, but decreased by molting (62.3% in pre-molting and 24.9% in post-molting hens). Moreover, pathogenic bacteria such as Enterococcus cecorum and Escherichia coli were more abundant in immediate post-molting hens than in pre-molting hens. Forced molting influenced the alpha diversity, with higher Chao1 (p = 0.012), phylogenetic diversity whole tree (p = 0.014), observed operational taxonomic unit indices (p = 0.006), and Simpson indices (p<0.001), which indicated that forced molting increased excreta bacterial richness of aged laying hens.

Conclusion

This study improves the current knowledge of bacterial community alterations in the excreta by forced molting in aged laying hens, which can provide increasing opportunity to develop novel dietary and management skills for improving the gastrointestinal health of aged laying hens after molting.

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons

Probiotics are bacterial species or assemblages that are applied to animals and plants with the intention of altering the microbiome in a beneficial way. Probiotics have been linked to positive health effects such as faster disease recovery times in humans and increased weight gain in poultry. Pigeon fanciers often feed their show pigeons probiotics with the intention of increasing flight performance. The objective of our study was to determine the effect of two different probiotics, alone and in combination, on the fecal microbiome of Birmingham Roller pigeons. We sequenced fecal samples from 20 pigeons divided into three probiotic treatments, including prior to, during, and after treatment. Pre-treatment and control group samples were dominated by Actinobacteria, Firmicutes, Proteobacteria, and Cyanobacteria. Administration of a probiotic pellet containing Enterococcus faecium and Lactobacillus acidophilus resulted in increase in average relative abundance of Lactobacillus spp. from 4.7 ± 2.0% to 93.0 ± 5.3%. No significant effects of Enterococcus spp. were detected. Probiotic-induced shifts in the microbiome composition were temporary and disappeared within 2 days of probiotic cessation. Administration of a probiotic powder in drinking water that contained Enterococcus faecium and three Lactobacillus species had minimal effect on the microbiome. We conclude that supplementing Birmingham roller pigeons with the probiotic pellets, but not the probiotic powder, temporarily changed the microbiome composition. A next step is to experimentally test the effect of these changes in microbiome composition on host health and physical performance.

Oral administration of Lactobacillus rhamnosus GG to newborn piglets augments gut barrier function in pre-weaning piglets

To understand the effects of Lactobacillus rhamnosus GG (ATCC 53103) on intestinal barrier function in pre-weaning piglets under normal conditions, twenty-four newborn littermate piglets were randomly divided into two groups. Piglets in the control group were orally administered with 2 mL 0.1 g/mL sterilized skim milk while the treatment group was administered the same volume of sterilized skim milk with the addition of viable L. rhamnosus at the 1st, 3rd, and 5th days after birth. The feeding trial was conducted for 25 d. Results showed that piglets in the L. rhamnosus group exhibited increased weaning weight and average daily weight gain, whereas diarrhea incidence was decreased. The bacterial abundance and composition of cecal contents, especially Firmicutes, Bacteroidetes, and Fusobacteria, were altered by probiotic treatment. In addition, L. rhamnosus increased the jejunal permeability and promoted the immunologic barrier through regulating antimicrobial peptides, cytokines, and chemokines via Toll-like receptors. Our findings indicate that oral administration of L. rhamnosus GG to newborn piglets is beneficial for intestinal health of pre-weaning piglets by improving the biological, physical, and immunologic barriers of intestinal mucosa.