The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids

Effects of Dietary Supplementation of gEGF on the Growth Performance and Immunity of Broilers

EGF has been shown to stimulate the growth of animals. In this study, the content of EGF in chicken embryos (gallus EGF, gEGF) aged from 1 to 20 days of incubation were determined by ELISA kit, and the 5-day-old chicken embryos with the highest content of 5593 pg/g were selected to make gEGF crude extracts. A total of 1500 1-day-old Xianju chickens were randomly divided into five groups with six replicates of 50 chickens each. The control group was fed a basal diet, and other treatment diets were supplemented with 4, 8, 16 and 32 ng/kg gEGF crude extract, respectively. The experiment lasted for 30 days. Chicks were harvested at the end of the experiment, and liver, spleen, thymus, bursa and serum samples were collected. Results showed that average daily gain (ADG) and average daily feed intake (ADFI) of 16 ng/kg group were higher than those in the control group (p < 0.05). The serum uric acid (UA) of the 16 ng/kg group was reduced (p < 0.01), and the serum alkaline phosphatase (AKP) of the 16 ng/kg group increased (p < 0.01). The gEGF extract also increased chick's antioxidant capacity, decreased malondialdehyde (MDA) and increased catalase (CAT) in the liver and serum of 16 ng/kg groups in compared to the control group (p < 0.01). Furthermore, immunity was improved by the addition of gEGF to broiler diets. The serum immunoglobin A (IgA) content of 8 and 16 ng/kg groups and the serum immunoglobin M (IgM) content of 4 and 8 ng/kg groups were increased (p < 0.05) compared to the control group. The bursa index of each experimental group was higher than the control group (p < 0.01). These findings demonstrate that the crude extract of gEGF prepared in this experiment could improve the growth performance, antioxidant capacity and immunity of broilers.

Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds

Opportunistic feeding and multiple other environment factors can modulate the gut microbiome, and bias conclusions, when wild animals are used for studying the influence of phylogeny and diet on their gut microbiomes. Here, we controlled for these other confounding factors in our investigation of the magnitude of the effect of diet on the gut microbiome assemblies of nonpasserine birds. We collected fecal samples, at one point in time, from 35 species of birds in a single zoo as well as 6 species of domestic poultry from farms in Guangzhou city to minimize the influences from interfering factors. Specifically, we describe 16S rRNA amplicon data from 129 fecal samples obtained from 41 species of birds, with additional shotgun metagenomic sequencing data generated from 16 of these individuals. Our data show that diets containing native starch increase the abundance of Lactobacillus in the gut microbiome, while those containing plant-derived fiber mainly enrich the level of Clostridium Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, the metagenome functions of the microbes (such as lipid metabolism and amino acid synthesis) were adapted to the different food types to achieve a beneficial state for the host. In conclusion, the covariation of diet and gut microbiome identified in our study demonstrates a modulation of the gut microbiome by dietary diversity and helps us better understand how birds live based on diet-microbiome-host interactions.IMPORTANCE Our study identified food source, rather than host phylogeny, as the main factor modulating the gut microbiome diversity of nonpasserine birds, after minimizing the effects of other complex interfering factors such as weather, season, and geography. Adaptive evolution of microbes to food types formed a dietary-microbiome-host interaction reciprocal state. The covariation of diet and gut microbiome, including the response of microbiota assembly to diet in structure and function, is important for health and nutrition in animals. Our findings help resolve the major modulators of gut microbiome diversity in nonpasserine birds, which had not previously been well studied. The diet-microbe interactions and cooccurrence patterns identified in our study may be of special interest for future health assessment and conservation in birds.

A practical guide to amplicon and metagenomic analysis of microbiome data

Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.

Microbial driven genetic variation in holobionts

Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.

Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output

Gut microbiota is known to influence the host’s health; an imbalance of the gut microbial community leads to various intestinal and non-intestinal diseases. Research on gut microbes of endangered birds is vital for their conservation. However, a thorough understanding of the gut microbiome composition present in crested ibises at different ages and its correlation with crested ibis reproductive capacity has remained elusive. Here, we used 16S rRNA gene sequencing to explore the fecal microbial structure of nestlings and adult birds, and the difference in gut microbiota between healthy and sterile crested ibises. We observed that (1) bacterial microbiota, alpha and beta diversity of one-day-old nestlings significantly distinguished from other nestlings; abundance of Proteobacteria decreased, while that of Fusobacteria increased with an increase in the age of the nestlings; (2) there was no significant difference in community composition among adult crested ibises aged one, two, three, and five years; (3) the abundance of Proteobacteria and alpha diversity indices were higher in sterile crested ibises than in healthy crested ibises; thus, Proteobacteria can act as a diagnostic biomarker of reproductive dysfunction in crested ibises. This study significantly contributes to the field of ecology and conservation, as it provides a platform for assessing the reproductive capacity of endangered crested ibises, based on the gut microbiota composition. Further studies may unravel additional factors influencing crested ibises’ reproductive health, which will further help the management and control of the crested ibis population.

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.

Effects of feed supplementation with 3 different probiotic Bacillus strains and their combination on the performance of broiler chickens challenged with Clostridium perfringens

The application of probiotics in broiler feed, to alleviate performance deficiencies due to mild infections by coccidia and Clostridium perfringens, is of increasing interest for the poultry industry. Therefore, our objective was to evaluate the capacity of 3 Bacillus strains and their combination as probiotics in vitro and in vivo. Thus, protein and carbohydrate degradation and C. perfringens growth inhibition capabilities were assessed by colometry measurement and an agar diffusion bioassay, respectively. A total of 2,250 1-day-old male broiler chicks were assigned to 5 dietary treatments: 1) non-probiotic-supplemented control (control); 2) control + DSM 32324 at 0.8 × 106 cfu/g of feed; 3) control + DSM 32325 at 0.5 × 106 cfu/g of feed; 4) control + DSM 25840 at 0.3 × 106 cfu/g of feed; and 5) control + DSM 32324 + DSM 32325 + DSM 25840 at 1.6 × 106 cfu/g of feed. A pathogenic field strain of C. perfringens was used to induce the necrotic enteritis challenge on day 19, 20, and 21. All birds and remaining feed were weighed on pen basis on day 0, 21, 35, and 42, to calculate BW gain and mortality-adjusted feed conversion. Mortality and mortality due to necrotic enteritis were recorded daily. On day 21, 45 birds per treatment were evaluated for macroscopic intestinal necrotic enteritis lesions. Performance data were statistically analyzed using an ANOVA and subjected to a least significant difference comparison. Necrotic enteritis lesion scores were statistically analyzed using nonparametric Kruskal-Wallis test. Dunn's test was used for treatment comparison. The tested strains showed different abilities of degrading protein and carbohydrates and inhibiting C. perfringens growth in vitro. The birds fed the multi-train combination presented significantly better performance and lower necrotic enteritis lesion score than those in the control group. Dietary supplementation with probiotics resulted in significantly lower necrotic enteritis mortality. The results demonstrate the suitability of the evaluated Bacillus multistrain combination as an effective probiotic in C. perfringens-challenged chickens.

A critical assessment of gene catalogs for metagenomic analysis

MOTIVATION

Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses.

RESULTS

As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research.

AVAILABILITY AND IMPLEMENTATION

All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Disequilibrium in chicken gut microflora with avian colibacillosis is related to microenvironment damaged by antibiotics

The avian colibacillosis outbreak is a disease that threatens public health, poultry production, and economic interests, even after antibiotic feed addition. It is known that avian pathogenic E. coli is a major pathogenic factor; however, the systemic characteristics of gut flora in disease samples and how pathogens grow remain unknown. To study these issues in depth, we used the whole microbial genome shotgun sequencing technique to compare entire microbes in diseased and healthy broiler chickens. We found that it was not only E. coli that increased substantially, but most pathogenic flora also increased significantly in diseased samples. Subsequently, we proved that aminoglycoside antibiotic resistance genes were mainly found in non-E. coli strains. This suggests that E. coli survival under antibiotic stress was due to the cooperative resistance from non-E. coli strains. Among all these increasing strains, attaching and effacing pathogens could damage host intestinal epithelial cells to release oxygen in the gut to make the microenvironment more adaptable for E. coli strains. Furthermore, we observed that the functions of the T4SS/T6SS secretion system were dramatically enhanced, which could help E. coli to compete and enlarge their living spaces. Ultimately, pathogenic E. coli accumulated to cause avian colibacillosis. This study provides a new insight into intestinal microecology in diseased individuals, which would propose new treatment options for avian colibacillosis from a metagenome perspective.

Supplementation of Bacillus subtilis GM5 enhances broiler body weight gain and modulates cecal microbiota

We investigated the effect of the strain Bacillus subtilis GM5 on growth, feed conversion, and the composition of cecum microbiota in broiler chickens. Half of which received a control diet, while the other half was fed a diet supplemented with GM5 spores. Cecal contents on days 1, 10, and 42 were subjected to metataxonomic analysis. Principal Component Analysis showed that the control and probiotic groups formed three separate clusters, indicating changes, which occurred gradually in microbial communities. On day 1, Firmicutes (53.87-57.61%) and Proteobacteria (43.77-38.93%) were prevalent in both groups, whereas samples of days 10 and 42 were predominantly occupied by Firmicutes (54.55-81.79%) and Bacteroidetes (26.94-30.45%). In the group of chickens treated with probiotic, the average daily gain in body weight was higher, while feed conversion decreased by 1.44%. A surge in the presence of beneficial bacteria of the Ruminococcaceae family was observed. The introduction of the probiotic led to an elevated Firmicutes/Bacteroidetes ratio, which positively correlated with chickens' bodyweight (Spearman ρ = 1.0, P < 0.05). Supplementing broiler feed with B. subtilis GM5 spores leads to improved feed intake and digestibility, which is paramount in reducing the cost of the final product. Thus, the probiotic strain GM5 modulates the cecal microbiota of broiler chickens and increases microbial diversity, which is well exhibited on the 42nd day.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02634-2.

A Comparison Study of the Caecum Microbial Profiles, Productivity and Production Quality of Broiler Chickens Fed Supplements Based on Medium Chain Fatty and Organic Acids

Simple Summary

The ban of growth promoters in poultry farming in the European Union has resulted in the development of alternatives. Among these alternatives, medium chain fatty acids (MCFAs) or organic acids (OAs) are considered to be suitable for in-feed use. However, their effect on microbiota modulation and the meat quality of broiler chickens are still under-investigated. The aim of this study was to estimate the influence of MCFAs and OAs supplements on the caecum microbial profiles, productivity and production quality characteristics of broiler chickens. The 42-days experiment was conducted using 900-day-old broiler chickens, allocated into three groups, consisting of 300 birds per group. The results indicated that the addition of OAs results in a more appropriate environment in the caecum for beneficial microorganisms rather than diets supplemented with MCFAs. These positive changes led to a higher efficiency of poultry productivity (higher body weight and lower mortality); however, for most of the analysed broilers’, technological parameters were not considerably influenced by treatments.

Abstract

The aim of this study was to evaluate the influence of medium chain fatty acids (MCFAs) and organic acids (OAs) supplements on the caecum microbial profiles, productivity and production quality characteristics of broiler chickens (BCs). BC (900 chicks) were attributed to three groups: (i) control; (ii) MCFAs group (BCs fed with feed supplemented with MCFAs); (iii) OAs group (BCs fed with feed supplemented with OAs). Broilers were slaughtered at the end of the trial (42 days old), and the caecum microbial profiles, productivity and production quality characteristics were analysed. Supplementation with OAs resulted in a more appropriate environment in the caecum for beneficial microorganisms than with a diet supplemented with MCFAs. This was supported by data on the presence of higher amounts and an increased species variety of probiotic bacteria (Lactobacillus and Bifidobacterium) in the caecum of birds. The above-mentioned changes of the caecum microbiota led to significantly higher villus height (p = 0.003) of the OAs broiler group and significantly lower crypt depth (p = 0.037). Notwithstanding the significant increase of acetic, propionic, isobutyric, butyric, isovaleric, and valeric acids that were established in caecum samples from the MCFAs group, better parameters of broiler production performance (higher body weight and lower mortality) and carcass traits (higher both thigh and shin muscles with skin and bone weight; both shin muscles without skin and bone weight; abdominal fat yield) were found in the OAs-treated group. For chemical, physical and technological characteristics of breast meat samples, increased yellowness and water holding capacity by 14.7% and 2.3%, respectively, were found in MCFAs group samples. A more appropriate environment in the caecum for beneficial microorganisms could be obtained when BCs were fed with OAs supplement, comparing to MCFAs, and these positive changes were associated with higher efficiency of poultry production.

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.

Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found

Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.

A microbial gene catalog of anaerobic digestion from full-scale biogas plants

BACKGROUND

Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood.

FINDINGS

In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination.

CONCLUSIONS

This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

Lactobacillus salivarius ameliorated Mycoplasma gallisepticum-induced inflammatory injury and secondary Escherichia coli infection in chickens: Involvement of intestinal microbiota

Mycoplasma gallisepticum (MG) infection alone or in combination with other pathogens have brought huge economic losses to the poultry industry. The intestinal microbiota plays a critical role in host defence against respiratory infection. To explore the role of intestinal microbiota in MG-induced inflammation-mediated lung injury and secondary Escherichia coli infection, MG infection model and fecal microbiota transplantation model were developed. The results showed that MG infection changed gut microbiota composition along with lung inflammation injury. Fecal microbiota transplantation from chickens infected with MG to antibiotics cocktail treated chickens decreased host defense against Escherichia coli due to impaired intestinal mucosal barrier, downregulated the mRNA expression levels of host defense enzymes and blocked autophagic flux. Lactobacillus salivarius intake alleviated lung inflammation injury caused by MG infection and increased host defense against Escherichia coli by improved gut microbiota composition. These results highlighted the role of gut microbiota in MG-infection induced lung inflammation injury and secondary infection that offered a new strategy for preventive intervention against MG infection.

Influence of different elicitors on BIA production in Macleaya cordata

Sanguinarine (SAN) and chelerythrine (CHE) have been widely used as substitutes for antibiotics for decades. For a long time, SAN and CHE have been extracted from mainly Macleaya cordata, a plant species that is a traditional herb in China and belongs to the Papaveraceae family. However, with the sharp increase in demand for SAN and CHE, it is necessary to develop a new method to enhance the supply of raw materials. Here, we used methyl jasmonate (MJ), salicylic acid (SA) and wounding alone and in combination to stimulate aseptic seedlings of M. cordata at 0 h, 24 h, 72 h and 120 h and then compared the differences in metabolic profiles and gene expression. Ultimately, we found that the effect of using MJ alone was the best treatment, with the contents of SAN and CHE increasing by 10- and 14-fold, respectively. However, the increased SAN and CHE contents in response to combined wounding and MJ were less than those for induced by the treatment with MJ alone. Additionally, after MJ treatment, SAN and CHE biosynthetic pathway genes, such as those encoding the protopine 6-hydroxylase and dihydrobenzophenanthridine oxidase enzymes, were highly expressed, which is consistent with the accumulation of SAN and CHE. At the same time, we have also studied the changes in the content of synthetic intermediates of SAN and CHE after elicitor induction. This study is the first systematic research report about using elicitors to increase the SAN and CHE in Macleaya cordata.

Fermented traditional Chinese medicine alters the intestinal microbiota composition of broiler chickens

For a long time, phytogenic resources have been widely used as substitutes for antibiotics in livestock production. However, few studies have examined the relationship between the intestinal microbiota and fermented herbal medicines. Here, 252 Arbor Acres broiler plus broiler chickens were randomly assigned to a control group, which was fed a basal diet; an unfermented healthy chicken powder group (JJS) fed a basal diet containing 20 g/kg JJS; or one of 5 fermented JJS groups, which were fed a basal diet containing 20 g/kg JJS, fermented with by 5 different bacterial strains for 42 days. The growth performances of the different groups were measured and the changes in the intestinal microbiota were analyzed. The body weight gain in the Bacillus subtilis group (Bs) was the highest among the 6 groups, while the feed conversion ratio (FCR) was best with Z. rouxii fermentation. The result indicated that products of JJS fermentation products of JJS by B. subtilis and Z. rouxii had important effects on chicken growth performance. The foregut and hindgut microbial communities of Bs, Zr, the control group and the JJS group, were collected for 16S rDNA sequencing. The results showed that JJS and its fermentation products mainly acted on the foregut and had little effect on the hindgut, and Z. rouxii fermentation products can increased the diversity in the foregut microbial community. In addition, the relative abundance of Bifidobacterium in the foregut of the Z. rouxii group was significantly increased, which may be an important factor in promoting growth.

Dysbiosis of gut microbiota in patients with esophageal cancer

A number of studies have identified that gut microbiota influences the development of cancer. However, there is little known about gut microbiota and esophageal cancer (EC). The aim of this study was to investigate the gut microbiota profile associated with EC. In this study, 23 patients with EC and 23 sex- and age-matched healthy controls (NC) were recruited between July 2019 and August 2019 at Huai'an First People's Hospital (Huai'an, China) and the gut microbiota was analyzed by 16S rRNA gene sequencing of fresh stool samples. We found that the microbial richness of intestinal flora in patients with EC were higher than NC, whereas evenness did not change obviously. Principal coordinate analysis (PCoA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis both revealed that a distinct separation in bacterial community composition between the EC and NC. At the phylum level, the EC group showed significantly higher abundances of Firmicutes and Actinobacteria, but a lower Bacteroidetes than NC. At the genus level, a significantly increased abundance of Streptococcus, Bifidobacterium, Subdoligranulum, Blautia, Romboutsia, Collinsella, Paeniclostridium, Dorea, and Atopobium were observed in EC patients, while Lachnospira, Bacteroides, Agathobacter, Lachnoclostridium, Parabacteroides, Paraprevotella, Butyricicoccus, Tyzzerella, Fusicatenibacter, and Sutterella were reduced. Receiver operating characteristic (ROC) analysis revealed that Lachnospira, Bacteroides, Streptococcus, and Bifidobacterium both achieved a high accuracy in EC diagnosis (area under the curve was more than 0.85), and the Lachnospira was found to be the best classifier. This study firstly characterized the gut microbiota composition of EC patients and screened out the optimal potential microbiota biomarkers for EC diagnosis. It may provide a fundamental reference for further studies on the gut microbiome for the diagnosis and treatment of EC.

Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers

Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A-E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.

A novel microbiome metabolic modulator improves the growth performance of broiler chickens in multiple trials and modulates targeted energy and amino acid metabolic pathways in the cecal metagenome

A meta-analysis of 19 floor-pen trials (579 replicate pen observations) in diverse geographies, basal diets, seasons, and medication programs was carried out to evaluate the effects of 2 precision glycan microbiome metabolic modulators (MMM1 and MMM2) on the performance of broiler chickens. In each trial, negative-control (NC) diets were compared with either MMM1 (14 trials) or MMM2 (8 trials), supplemented at an intended dose of 500 g/MT from hatch to 31 to 42 d. A dose response of MMM2 was evaluated in 8 trials at doses of 100, 250, 500, and 1,000 g/MT, not all present in each trial. Linear mixed-effect models were constructed for the final BW, cumulative feed intake, feed conversion ratio (FCR) corrected by mortality and BW (cFCR), and mortality, with Treatment as the fixed effect, nested random effects of Trial and Block, and adjustments for heterogeneity of variances. A significance level of P < 0.05 was used. In one of the studies, cecal content samples were collected at 42 d for analysis of microbiome gene abundance. Microbiome metabolic modulator 2 exhibited a reduction of the cFCR of 0.06 g feed/g BW gain compared with the NC and 0.03 g feed/g BW gain compared with MMM1, whereas MMM1 reduced the cFCR by 0.03 g feed/g BW gain compared with NC. Both MMM1 and MMM2 increased the final BW compared with the NC by 43 and 48 g/bird, respectively, with no difference among them. Compared with NC, feed intake was increased by MMM1 (+51 g/bird) and reduced by MMM2 (−74 g/bird). A one-directional dose response of the MMM2 ingredient was observed for the final BW (increasing) and cFCR (decreasing), whereas the feed intake response reached a minimum at 500 g/MT. The metagenomic analysis confirmed an increase in the abundance of genes belonging to the acrylate pathway, which is involved in propionate production, as well as arginine-N-succinyl transferase which is involved in the catabolism of arginine, in response to MMM2. Differential glycan structures of the MMM had an impact on the size and consistency of performance effects in broilers.

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 5,596 metagenome-assembled genomes (MAGs) from the gut metagenomes of 180 predominantly wild animal species representing 5 classes, in addition to 14 existing animal gut metagenome data sets. The MAGs comprised 1,522 species-level genome bins (SGBs), most of which were novel at the species, genus, or family level, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1,986 diverse biosynthetic gene clusters; only 23 clustered with any MIBiG database references. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene data sets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to the vertebrate gut.IMPORTANCE Microbiome studies on a select few mammalian species (e.g., humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in the gut of other vertebrates. We studied the gut microbiomes of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish. Unfortunately, we found that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates. To increase database representation, we applied advanced metagenome assembly methods to our animal gut data and to many public gut metagenome data sets that had not been used to obtain microbial genomes. Our resulting genome and gene cluster collections comprised a great deal of novel taxonomic and genomic diversity, which we extensively characterized. Our findings substantially expand what is known of microbial genomic diversity in the vertebrate gut.

Adaptive response to a future life challenge: consequences of early-life environmental complexity in dual-purpose chicks

Conditions in early life play profound and long-lasting effects on the welfare and adaptability to stress of chickens. This study aimed to explore the hypothesis that the provision of environmental complexity in early life improves birds' adaptive plasticity and ability to cope with a challenge later in life. It also tried to investigate the effect of the gut-brain axis by measuring behavior, stress hormone, gene expression, and gut microbiota. One-day-old chicks were split into 3 groups: (1) a barren environment (without enrichment items) group (BG, n = 40), (2) a litter materials group (LG, n = 40), and (3) a perches with litter materials group (PLG, n = 40). Then, enrichment items were removed and simulated as an environmental challenge at 31 to 53 d of age. Birds were subjected to a predator test at 42 d of age. In the environmental challenge, when compared with LG, PLG birds were characterized by decreased fearfulness, lower plasma corticosterone, improved gut microbial functions, lower relative mRNA expression of GR, and elevated mRNA expressions of stress-related genes CRH, BDNF, and NR2A in the hypothalamus (all P < 0.05). Unexpectedly, the opposite was true for the LG birds when compared with the BG (P < 0.05). Decreased plasma corticosterone and fearfulness were accompanied by altered hypothalamic gene mRNA expressions of BDNF, NR2A, GR, and CRH through the HPA axis in response to altered gut microbial compositions and functions. The findings suggest that gut microbiota may integrate fearfulness, plasma corticosterone, and gene expression in the hypothalamus to provide an insight into the gut-brain axis in chicks. In conclusion, having access to both perches and litter materials in early life allowed birds to cope better with a future challenge. Birds in perches and litter materials environment may have optimal development and adaptive plasticity through the gut-brain axis.

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease

Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.

Propionate inhibits fat deposition via affecting feed intake and modulating gut microbiota in broilers

As one of the 3 main short-chain fatty acids, the role of propionate in chicken fat metabolism is largely unknown. In this study, we demonstrated that dietary supplementation of coated sodium propionate (SP) moderately inhibits fat deposition in broiler chickens, as evidenced by the decreased adipocyte mean area (P < 0.01), the lowered triglyceride content in abdominal fat tissue (P < 0.01), and the reduced transcription of several lipogenic genes in liver and abdominal fat tissues (P < 0.05). Surprisingly, the propionate content was not significantly elevated either in serum or in the cecal chyme by SP administration (P > 0.05). However, SP application significantly decreased the average daily feed intake of broilers (P < 0.05). In addition, the composition of the cecal microbial communities was altered, with the ratio of Firmicutes to Bacteroidetes decreasing in particular (P < 0.05). At the genus level, SP application increased the richness of Alistipes, Lactobacillus, and Bifidobacterium, while reduced the abundance of Lachnospiraceae and Helicobacter significantly (P < 0.05). Moreover, in vitro experiments indicated that, although physiological concentrations of propionate (0.01 to 0.1 mmol) upregulated or downregulated the transcription of some fat synthesis-associated genes (P < 0.05), they did not significantly affect the triglyceride accumulation in hepatocytes and adipocytes (P > 0.05). These results suggest that feed supplementation with SP inhibits fat deposition in broilers by reducing feed and caloric intake, but not via direct regulation on hepatic fat synthesis or adipocytic fat deposition. Alteration in the relative populations of the gut microflora suggests that SP may have gut health implications.

RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing

Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.

Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165 T. Methods: For the possible novel strain SW165 T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989 T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45 oC and pH 6.0-7.5 respectively.  This strain produced acetic acid as the primary fermentation product. Major fatty acids were C 12:0, C 14:0, C 14:0 DMA and summed feature 1 (C 13:1 at 12-13 and C 14:0 aldehyde). Strain SW165 T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165 T and DSM 13989 T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165 T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165 ^T.

Methods: For the possible novel strain SW165 ^T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis.

Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989 ^T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45 ^oC and pH 6.0-7.5 respectively.  This strain produced acetic acid as the primary fermentation product. Major fatty acids were C _12:0, C _14:0, C _14:0 DMA and summed feature 1 (C _13:1 at 12-13 and C _14:0 aldehyde). Strain SW165 ^T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165 ^T and DSM 13989 ^T were only 17.6 ± 5.3 and 74.35%, respectively.

Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165 ^T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

Background

Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research. Both supervised and unsupervised machine learning methods have been employed in binning. Genome binning belonging to unsupervised method clusters contigs into individual genome bins by machine learning methods without the assistance of any reference databases. So far a lot of genome binning tools have emerged. Evaluating these genome tools is of great significance to microbiological research. In this study, we evaluate 15 genome binning tools containing 12 original binning tools and 3 refining binning tools by comparing the performance of these tools on chicken gut metagenomic datasets and the first CAMI challenge datasets.

Results

For chicken gut metagenomic datasets, original genome binner MetaBat, Groopm2 and Autometa performed better than other original binner, and MetaWrap combined the binning results of them generated the most high-quality genome bins. For CAMI datasets, Groopm2 achieved the highest purity (> 0.9) with good completeness (> 0.8), and reconstructed the most high-quality genome bins among original genome binners. Compared with Groopm2, MetaBat2 had similar performance with higher completeness and lower purity. Genome refining binners DASTool predicated the most high-quality genome bins among all genomes binners. Most genome binner performed well for unique strains. Nonetheless, reconstructing common strains still is a substantial challenge for all genome binner.

Conclusions

In conclusion, we tested a set of currently available, state-of-the-art metagenomics hybrid binning tools and provided a guide for selecting tools for metagenomic binning by comparing range of purity, completeness, adjusted rand index, and the number of high-quality reconstructed bins. Furthermore, available information for future binning strategy were concluded.

Assessment of Probiotic Properties of Lactobacillus salivarius Isolated From Chickens as Feed Additives

The continued use of sub-therapeutic antibiotics as feed additives in the poultry industry improved health and growth performance. However, the resulting antibiotic resistance increasingly becomes a major threat to public health. Probiotics are promising alternatives for the antibiotics used in poultry industry. The aim of this study was to evaluate the probiotic properties of Lactobacillus salivarius as feed additive in chickens. White leghorn chickens were randomly assigned to experimental groups. Effects of Lactobacillus salivarius supplementation on growth performance, resistance to Escherichia coli O78 challenge and heat-stress, and immune response after vaccinated with attenuated infectious bursal disease virus (IBDV) vaccine were determined. The results showed that Lactobacillus salivarius supplementation improved growth performance, such as weight and longer shank length, increased relative weights of the immune organs and decreased concentrations of odor-causing compounds. In addition, Lactobacillus salivarius supplementation alleviated organ injury caused by Escherichia coli O78 challenge and heat stress. Furthermore, Lactobacillus salivarius results in enhanced immune response after IBDV vaccine immunization, enhanced specific antibody and IFN-γ production, and lymphocyte proliferation. Our results revealed a tremendous potential of Lactobacillus salivarius as antibiotics' substitute in poultry production.

The Rhizosphere Microbiome of Mikania micrantha Provides Insight Into Adaptation and Invasion

Mikania micrantha is a noxious invasive plant causing enormous economic losses and ecological damage. Soil microbiome plays an important role in the invasion process of M. micrantha, while little is known about its rhizosphere microbiome composition and function. In this study, we identified the distinct rhizosphere microbial communities of M. micrantha, by comparing them with those of two coexisting native plants (Polygonum chinense and Paederia scandens) and the bulk soils, using metagenomics data from field sampling and pot experiment. As a result, the enrichment of phosphorus-solubilizing bacteria Pseudomonas and Enterobacter was consistent with the increased soil available phosphorus in M. micrantha rhizosphere. Furthermore, the pathogens of Fusarium oxysporum and Ralstonia solanacearum and pathogenic genes of type III secretion system (T3SS) were observed to be less abundant in M. micrantha rhizosphere, which might be attributed to the enrichment of biocontrol bacteria Catenulispora, Pseudomonas, and Candidatus Entotheonella and polyketide synthase (PKS) genes involved in synthesizing antibiotics and polyketides to inhibit pathogens. These findings collectively suggested that the enrichment of microbes involved in nutrient acquisition and pathogen suppression in the rhizosphere of M. micrantha largely enhances its adaptation and invasion to various environments.

Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers

BACKGROUND

Glucose oxidase (GOD), an aerobic dehydrogenase, has been used as an antibiotic substitute in feed. A study was conducted to evaluate the differential effects of 2 different GODs fermented by Aspergillus niger or Penicillium amagasakiense on caecal microbiota and to further illuminate the potential roles of changes in the gut microbiota in regulating the growth performance and meat quality of broiler chickens.

RESULTS

A total of 420 one-day-old healthy Arbor Acres broilers were randomly assigned to 4 treatments: the control group, the antibiotic growth promoter (AGP) supplementation group, and the GOD-A and GOD-P (GODs produced by A. niger and P. amagasakiense, respectively) groups. As a result, supplementation with GOD produced by P. amagasakiense could significantly improve the average daily weight gain and average daily feed intake of broilers before 21 days of age by significantly increasing the enzymatic activities of jejunal amylase and those of ileal amylase, chymotrypsin, and lipase in 21-day-old broilers and could increase the enzymatic activities of duodenal amylase, jejunal amylase and lipase, and ileal chymotrypsin and lipase in 42-day-old broilers. Meanwhile, compared with AGP treatment, supplementation with GOD produced by P. amagasakiense significantly decreased the L value of 21-day-old broilers and the ΔpH and L* value of 42-day-old broilers, while supplementation with GOD produced by A. niger significantly increased the pH_24 h value of 21-day-old and 42-day-old broilers by reducing plasma malondialdehyde content. By using 16S rRNA sequencing, we found that the beneficial bacteria and microbiota in broilers were not disturbed but were improved by GOD supplementation compared with ADP treatment, including the genera Eubacterium and Christensenella and the species uncultured_Eubacterium_sp, Clostridium_asparagiforme, and uncultured_Christensenella_sp, which were positively related to the improved intestinal digestive enzymatic activities, growth performance, and meat quality of broilers.

CONCLUSION

The altered gut microbiota induced by supplementation with glucose oxidase produced by P. amagasakiense mediate better regulatory effects on the meat quality and growth performance of broilers than that induced by supplementation with glucose oxidase produced by A. niger.

Sanguinarine modulate gut microbiome and intestinal morphology to enhance growth performance in broilers

Sanguinarine is a bioactive compound as a quaternary benzophenanthridine alkaloid from plant of the Macleaya cordata, Papaveraceae family. The present study was conducted to investigate the effects of dietary sanguinarine supplementation on growth performance, serum biochemistry parameters, intestinal mucosal morphology and gut microbiome in yellow feathered broilers. Two hundred and seventy 1-d-old female broilers were randomly assigned to 3 treatments ① Basal diet (NG); ② Basal diet containing bacitracin methylene disalicylate (50mg/Kg diet) (ANT); ③ Basal diet containing sanguinarine (0.7 mg/ kg of feed) (SAG). The statistical results showed that dietary sanguinarine supplementation enhanced growth performance and decreased glucose, uric acid as well as urea nitrogen levels of broilers at 28d of age (P<0.05). The 16S rRNA gene sequence analysis revealed that sanguinarine significantly decreased the species from the phyla Bacteroidetes, and increased the species from phyla Firmicutes. Moreover, dietary sanguinarine supplementation improved mucosal morphology to achieve higher ratio of intestinal villus height to crypt depth (P < 0.05), and decreased the concentrations of TNF-α and IL-4 in jejunum mucosal. This study demonstrated that sanguinarine supplementation in the diet of yellow feathered broilers improved intestinal morphology and microbiota community structure to promote growth performance on 1-28d.

A novel apidaecin Api-PR19 synergizes with the gut microbial community to maintain intestinal health and promote growth performance of broilers

Background

Antibiotic growth promoters (AGPs) have been used as growth promoters to maintain animal intestinal health and improve feed efficiency in broilers by inhibiting pathogen proliferation. In view of the growing emergence of antibiotic-resistant pathogen strains and drug residue issues, novel treatments are increasingly required. This study aimed to compare two antimicrobial approaches for managing pathogen infection and maintaining animal intestinal health in broilers by supplying Apidaecin Api-PR19 and AGPs over 42 d of a feeding trial.

Results

Compared with the broilers that were only fed a corn-soybean basal diet (CON group), supplementation with Api-PR19 and AGP (respectively named the ABP and AGP groups) both increased the feed conversion efficiency. When compared with the AGP group, Api-PR19 supplementation could significantly increase the organ index of the bursa of fabricius and subtype H9 antibody level in broiler chickens. Moreover, when compared with the CON group, the intestinal villus height, intestinal nutrient transport, and intestinal sIgA content were all increased in the Api-PR19 group, while AGP supplementation was harmful to the intestinal villus height and intestinal nutrient transport. By assessing the antibacterial effect of Api-PR19 and antibiotics in vitro and in vivo, we found that Api-PR19 and antibiotics both inhibited the growth of pathogens, including Escherichia coli and Campylobacter jejuni. Furthermore, by using 16S rRNA gene sequencing, the beneficial bacteria and microbiota in broilers were not disturbed but improved by apidaecin Api-PR19, including the genera of Eubacterium and Christensenella and the species of uncultured_Eubacterium_sp, Clostridium_asparagiforme, and uncultured_Christensenella_sp, which were positively related to improved intestinal development, absorption, and immune function.

Conclusion

Apidaecin Api-PR19 treatment could combat pathogen infection and had little negative impact on beneficial bacteria in the gut compared to antibiotic treatment, subsequently improving intestinal development, absorption, and immune function.

Microbial Community and Short-Chain Fatty Acid Mapping in the Intestinal Tract of Quail

Simple Summary

Quail is an economically important type of poultry, valued for its high meat quality and abundant egg nutrition. It is also an important laboratory research animal, widely used in developmental biology and toxicology tests. Since the gut microbiota plays a vital role in the host’s growth and health, we investigated the microbiota inhabiting the duodenum, jejunum, ileum, cecum, and colorectum of quail in the present study, using 16S rRNA gene sequencing and qPCR. The concentrations of short-chain fatty acids (SCFAs) were evaluated using gas chromatography. We found that the microbiota in the cecum was different from other intestinal sections and the enriched inhabitants of SCFA-producing bacterial genera made cecum the core locations of SCFA production in quail. The results of this study will provide fundamental data for further quail microbiology and functional studies.

Abstract

Quail is raised throughout China for egg and meat production. To deeply understand the gastrointestinal microbial composition and metabolites of quail, the present study characterized the microbiota inhabiting five intestinal locations of eight-week-old quail using 16S rRNA gene sequencing and qPCR, and evaluated the concentrations of short-chain fatty acids (SCFAs) in each individual location using gas chromatography. The results showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Deferribacteres were the five most abundant phyla in the intestinal tract of quail. Firmicutes was largely dominant (>95%) in the small intestine, whereas Bacteroidetes increased significantly in the cecum (19.19%) and colorectum (8.09%). At the genus level, Lactobacillus was predominant in almost all sections (>50%) except in the cecum (7.26%), where Megamonas, Faecalibacterium, and Bacteroides were dominant. qPCR data indicated that the population sizes of both the total bacteria and proportions of the Firmicutes, Bacteroidetes, and Bacteroides group increased going from the proximal toward the distal end of the intestine in quail. The SCFA-producing bacterial genera Bacteroides, Faecalibacterium, Alistipes, Blautia, Parabacteroides, and Clostridium were of higher richness in the cecum and colorectum, where, accordingly, more SCFAs were produced. These findings will be helpful for the future study of quail microbiology, as well as its relationship with productive performance and health.

Organic acid blend supplementation increases butyrate and acetate production in Salmonella enterica serovar Typhimurium challenged broilers

The burden of enteric pathogens in poultry is growing after the ban of antibiotic use in animal production. Organic acids gained attention as a possible alternative to antibiotics due to their antimicrobial activities, improved nutrient metabolism and performance. The current study was conducted to evaluate the effectiveness of organic acid blend on broilers cecal microbiota, histomorphometric measurements, and short-chain fatty acid production in Salmonella enterica serovar Typhimurium challenge model. Birds were divided into four treatments, including a negative control, positive control challenged with S. Typhimurium, group supplemented with an organic acid blend, and birds supplemented with organic acid blend and Salmonella challenged. Results illustrate significant differences in feed conversion ratios and production efficiency factor between treatment groups, however, the influence of organic acid supplement was marginal. Organic acid blend significantly increased cecal acetic and butyric acids concentrations when compared to unsupplemented groups and resulted in minor alterations of intestinal bacterial communities.

The gut microbiota confers protection in the CNS against neurodegeneration induced by manganism

Among all types of pollution, heavy metals are considered the greatest threat to human health, and heavy metals are associated with an increased risk of cardiovascular disease, coronary heart disease and neurodegenerative disorders. Manganese (Mn) exposure is well reported to exert neurotoxicity and various neurodegenerative disorders, but the mechanisms are not clear. The gut microbiota plays a crucial role in the bidirectional gut-brain axis that integrates the gut and central nervous system (CNS) activities. The changes in chemical signaling, metabolism and gut microbiota associated with Mn exposure have provided deeper insight into the neurotoxic mechanism of Mn. We observed that Mn exposure increases host manganic bioaccumulation, and β-amyloid (Aβ), receptor-interacting protein kinase 3 (RIP3) and caspase-3 production in the brain, and causes hippocampal degeneration and necrosis. Mn exposure led to decreased gut bacterial richness, especially for Prevotellaceae, Fusobacteriaceae and Lactobacillaceae. In addition, Mn exposure altered the metabolism of tryptamine, taurodeoxycholic acid, β-hydroxypyruvic acid and urocanic acid. Meanwhile, we found correlations between the abundance of certain bacterial species and the level of tryptamine, taurodeoxycholic acid, β-hydroxypyruvic acid and urocanic acid. Fecal microbiome transplantation from normal rats could alleviate the neurotoxicity of Mn exposure by shaping the gut microbiota. Our findings highlight the role of gut dysbiosis-promoted neurotoxicity in Mn exposure and suggest a novel therapeutic strategy of remodeling the gut microbiota.

Microbiota and metabolome responses in the cecum and serum of broiler chickens fed with plant essential oils or virginiamycin

This study investigated the cecal microbiota and serum metabolite profile of chickens fed with plant essential oils (PEO) or virginiamycin (VIRG) using high-throughput 16S rRNA gene sequencing and untargeted metabolomics approach. The main aim of this work was to explore the biochemical mechanisms involved in the improved growth performance of antibiotics and their alternatives in animal production. The results showed that both PEO and VIRG treatment significantly increased the relative abundance of phyla Bacteroidetes and decreased the abundance of phyla Firmicutes and genus of Lactobacillus in cecal microbiota of chickens. Compared to the control group (CT group), the relative abundance of genus of Alistipes, unclassified Rikenellaceae, Roseburia, and Anaeroplasma was enriched in the PEO group; that of genus Bacteroides, Lachnospiraceae, and unclassified Enterobacteriaceae was enriched in the cecal microbiota of the VIRG group. Untargeted metabolomics analyses revealed that the PEO treatment modified 102 metabolites and 3 KEGG pathways (primary bile acid biosynthesis and phenylalanine metabolism) in the cecal microbiota, and 81 metabolites and relevant KEGG pathways (fructose and mannose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid.) in the serum of the chicken. Compared to the CT group, VIRG treatment group differed 217 metabolites and 10 KEGG pathways in cecal contents and 142 metabolites and 7 KEGG pathways in serum of chickens. Pearson’s correlation analysis showed that phyla Bacteroidetes and genus of Bacteroides, Alistipes, and unclassified Rikenellaceae (in the VIRG and PE group) were positively correlated with many lipid metabolites. However, phyla Firmicutes and genera Lactobacillus (higher in the CT group) were negatively correlated with the lipid and thymine metabolism, and positively correlated with hydroxyisocaproic acid, cytosine, and taurine. This study shows that dietary supplementation with PEO and VIRG altered the composition and metabolism profile of the cecal microbiota, modified the serum metabolism profile.

Supplementation of Lactobacillus plantarum or Macleaya cordata Extract Alleviates Oxidative Damage Induced by Weaning in the Lower Gut of Young Goats

Weaning usually leads to stress in livestock, which has a negative impact on their growth and development. Research on oxidative stress and inflammation induced by weaning has not been reported in goats. Here, we focused on oxidative stress profile and inflammation status of the lower gut (jejunum, ileum, and colon) of goats. First, we illustrated the status of antioxidant activity and inflammation in the intestine of young goats on pre-(2 weeks postnatal, 2 wk^pn) or post-(11 wk^pn, weaning at day 45 postnatal)-weaned period of young goats. Malondialdehyde (MDA) was higher (p < 0.0001) in jejunum and ileum of the young goats in 11 wk^pn than that in 2 wk^pn, whereas superoxide dismutase (SOD) activity was lower (p = 0.012) in the lower gut of the young goats with 11 wk^pn than that in 2 wk^pn. Furthermore, we intended to explore the protective influence of a probiotic additive (Lactobacillus plantarum (LAC) P-8, 10 g/d) and a prebiotic additive (Sangrovit^®, Macleaya cordata (MAC) extract 3.75% w/w premix, 0.3 g/d) on intestinal oxidative stress and inflammation status of early-weaned young goats (average weights of 5.63 ± 0.30 kg, weaned on d 45 postnatal). We observed that LAC reduced MDA in jejunum and ileum (p < 0.0001), increased SOD activity in ileum (p < 0.01), and increased glutathione peroxidase (GSH-Px) activity in jejunum (p < 0.05). Similarly, MAC reduced MDA contents (p < 0.0001), increased SOD activities (p < 0.01) in both of ileum and jejunum, and increased GSH-Px activity (p < 0.05) in jejunum. However, there were no differences in feed intake, average daily gain, inflammation parameters (interleukin 2 and interleukin 6), and colon oxidative stress profile (MDA, SOD, or GSH-Px) among treatments. These results provide evidence that weaning induces oxidative damage in the lower gut of young goats, and the oxidative damage in the small intestine can be reduced by adding the addition of LAC or MAC in diets depending on the region of the lower gut.

Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications

Sustainable poultry practices are needed to maintain an adequate supply of poultry products to the increasing human population without compromising human wellbeing. In order to achieve the understanding of the core microbiome that assumes an imperative role in digestion, absorption, and assimilation of feed as well as restrict the growth of pathogenic strains, a proper meta-data survey is required. The dysbiosis of the core microbiome or any external infection in chickens leads to huge losses in the poultry production worldwide. Along with this, the consumption of infected meat also impacts on human health as chicken meat is a regular staple in many diets as a vital source of protein. To tackle these losses, sub-therapeutic doses of antibiotics are being used as a feed additive along with other conventional approaches including selective breeding and modulation in feed composition. Altogether, these conventional approaches have improved the yield and quality of poultry products, however, the use of antibiotics encompasses the risk of developing multi-drug resistant pathogenic strains that can be harmful to human beings. Thus, there is an urgent need to understand the chicken microbiome in order to modulate chicken gut microbiome and provide alternatives to the conventional methods. Although there is now emerging literature available on some of these important microbiome aspects, in this article, we have analysed the relevant recent developments in understanding the chicken gut microbiome including the establishment of integrated gene catalogue for chicken microbiome. We have also focussed on novel strategies for the development of a chicken microbial library that can be used to develop novel microbial consortia as novel probiotics to improve the poultry meat production without compromising human health. Thus, it can be an alternative and advanced step compared to other conventional approaches to improve the gut milieu and pathogen-mediated loss in the poultry industry.

The association between microbial community and ileal gene expression on intestinal wall thickness alterations in chickens

The dynamic development of the animal intestine with a concurrent succession of microbiota and changes in microbial community and metabolite spectrum can exert far-reaching effects on host physiology. However, the precise mechanism of mutual response between microbiota and the gut is yet to be fully elucidated. Broilers with varying developmental degrees of intestinal wall thickness were selected, and they were divided into the thick group (H type) and the thin group (B type), using multiomics data integration analysis to reveal the fundamental regulatory mechanisms of gut–microbiota interplay. Our data showed, in broilers with similar body weight, the intestinal morphological parameters were improved in H type and the diversity of microbial communities is distinguishable from each other. The beneficial bacteria such as Bifidobacterium breve was increased whereas avian endogenous retrovirus EAV-HP was decreased in the H type compared with the B type. Furthermore, microbial metabolic potentials were more active, especially the biosynthesis of folate was improved in the H type. Similarly, the consolidation of absorption, immunity, metabolism, and development was noticed in the thick group. Correlation analysis indicated that the expression levels of material transport and immunomodulatory-related genes were positively correlated with the relative abundance of several probiotics such as B. breve, Lactobacillus saerimneri, and Butyricicoccus pullicaecorum. Our findings suggest that the chickens with well-developed ileal thickness own exclusive microbial composition and metabolic potential, which is closely related to small intestinal morphogenesis and homeostasis.

Characteristics of the fecal microbiota of high- and low-yield hens and effects of fecal microbiota transplantation on egg production performance

The microbiota that resides in the digestive tract plays pivotal role in maintaining intestinal environmental stability by promoting nutrition digestion and intestinal mucosal immunity. However, whether the intestinal microbiota in laying hens affects egg laying- performance is not known. In this study, 16S rDNA gene sequencing and fecal microbiota transplantation were used to determine the structure of the intestinal microbiota and the effect of the intestinal microbiota on egg production. The results revealed that Firmicutes were dominant in both the H (high egg laying rates) and L (low egg laying rates) groups, while Bacteroides, Actinobacteria and Proteobacteria were significantly enriched in the L group compared to the H group. The laying rates were weakly affected in H hens transplanted with the fecal microbiota from L hens, except for temporary fluctuation, while the egg laying rates were significantly increased in L hens transplanted with the fecal microbiota from H hens. Therefore, we concluded that the population structure of the intestinal microbiota varied between the H and L groups, and the intestinal microbiota of high-yield laying hens had significant effects on low-yield laying hens performance.

Galacto-Oligosaccharides Modulate the Juvenile Gut Microbiome and Innate Immunity To Improve Broiler Chicken Performance

Improvements in growth performance and health are key goals in broiler chicken production. Inclusion of prebiotic galacto-oligosaccharides (GOS) in broiler feed enhanced the growth rate and feed conversion of chickens relative to those obtained with a calorie-matched control diet. Comparison of the cecal microbiota identified key differences in abundances of Lactobacillus spp. Increased levels of Lactobacillus johnsonii in GOS-fed juvenile birds at the expense of Lactobacillus crispatus were linked to improved performance (growth rate and market weight). Investigation of the innate immune responses highlighted increases of ileal and cecal interleukin-17A (IL-17A) gene expression counterposed to a decrease in IL-10. Quantification of the autochthonous Lactobacillus spp. revealed a correlation between bird performance and L. johnsonii abundance. Shifts in the cecal populations of key Lactobacillus spp. of juvenile birds primed intestinal innate immunity without harmful pathogen challenge.IMPORTANCE Improvements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations while mitigating the withdrawal of antibiotic growth promoters. Prebiotic galacto-oligosaccharides (GOS) are manufactured as a by-product of dairy cheese production and can be incorporated into the diets of juvenile chickens to improve their health and performance. This study investigated the key mechanisms behind this progression and pinpointed L. johnsonii as a key species that facilitates the enhancements in growth rate and gut health. The study identified the relationships between the GOS diet, L. johnsonii intestinal populations, and cytokine immune effectors to improve growth.

Sanguinarine metabolism and pharmacokinetics study in vitro and in vivo

Sanguinarine (SA) is a benzo[c] phenanthridine alkaloid which has a variety of pharmacological properties. However, very little was known about the pharmacokinetics of SA and its metabolite dihydrosanguinarine (DHSA) in pigs. The purpose of this work was to study the intestinal metabolism of SA in vitro and in vivo. Reductive metabolite DHSA was detected during incubation of SA with intestinal mucosa microsomes, cytosol, and gut flora. After oral (p.o.) administration of SA, the result showed SA might be reduced to DHSA in pig intestine. After i.m. administration, SA and DHSA rapidly increased to reach their peak concentrations (C_max , 30.16 ± 5.85, 5.61 ± 0.73 ng/ml, respectively) at 0.25 hr. Both compounds were completely eliminated from the plasma after 24 hr. After single oral administration, SA and DHSA rapidly increased to reach their C_max (3.41 ± 0.36, 2.41 ± 0.24 ng/ml, respectively) at 2.75 ± 0.27 hr. The half-life (T_1/2 ) values were 2.33 ± 0.11 hr and 2.20 ± 0.12 hr for SA and DHSA, respectively. After multiple oral administration, the average steady-state concentrations (C_ss ) of SA and DHSA were 3.03 ± 0.39 and 1.42 ± 0.20 ng/ml. The accumulation indexes for SA and DHSA were 1.21 and 1.11. The work reported here provides important information on the metabolism sites and pharmacokinetic character of SA. It explains the reasons for low toxicity of SA, which is useful for the evaluation of its performance.

Effects of Added Dietary Fiber and Rearing System on the Gut Microbial Diversity and Gut Health of Chickens

It is of merit to study the appropriate amount of dietary fiber to add to free-range chickens' feed to improve their microbial diversity and gut health in times of plant fiber deprivation. Lignocellulose is a useful source of dietary fiber, and its positive effects on the growth performance and laying performance of chickens has already been proven. However, few researchers have researched the effects of adding it on the gut microbiota of chickens. In this research, we added three different levels of eubiotic lignocellulose (0%, 2%, and 4%) to the feed of caged and free-range Bian chickens from September to November, aiming to observe the effects of added dietary fiber and different rearing systems on the gut microbial diversity and gut health of chickens, as well as to determine an appropriate amount of lignocellulose. The results showed that adding dietary fiber increased the thickness of the cecum mucus layer and the abundance of Faecalibacterium and Faecalibacterium in caged chickens, and 4% lignocellulose was appropriate. In addition, adding lignocellulose increased the microbial diversity and the abundance of the butyrate-producing bacteria Faecalibacterium and Roseburia in fee-range chickens. The α-diversity and the length of the small intestine with 2% lignocellulose in free-range chickens were better than with 2% lignocellulose in caged chickens. Maybe it is necessary to add dietary fiber to the feed of free-range chickens when plant fibers are lacking, and 2% lignocellulose was found to be appropriate in this experiment. In addition, compared with caged chickens, the free-range chickens had a longer small intestine and a lower glucagon like peptide-1 (GLP-1) level. The significant difference of GLP-1 levels was mainly driven by energy rather than short chain fatty acids (SCFAs). There was no interaction between added dietary fiber and the rearing system on SCFAs, cecum inner mucus layer, and GLP-1.

Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions

RNA sequencing was used to profile the liver transcriptome of a Korean commercial chicken (Hanhyup) at two different environments (Korea and Kyrgyzstan) to investigate their role during acclimatization into different climatic conditions. Ten samples from each location were analyzed to identify candidate genes that respond to environmental changes such as altitude, humidity, temperature, etc. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) <0.05 and fold change (FC) ≥2, we found 315 genes were DE. Out of 315 DE genes, 174 and 141 were up- and down-regulated respectively in the Kyrgyz environment. Gene ontology (GO) enrichment analysis showed that the differentially expressed genes (DEGs) were associated with energy metabolism such as pyruvate and lactate metabolic processes, and glycerol catabolic process. Similarly, KEGG pathway analysis indicated pyruvate metabolism, glycolysis/gluconeogenesis, biosynthesis, citrate cycles were differentially enriched in the Kyrgyz environment. DEGs like TSKU, VTG1, SGK, CDK2, etc. in such pathways are highly involved in the adaptation of organisms into diverse climatic conditions. Our investigation may serve as a resource for the chicken industry, especially in exporting Hanhyup chicken from Korea to other countries.

Short-term feeding of probiotics and synbiotics modulates caecal microbiota during Salmonella Typhimurium infection but does not reduce shedding and invasion in chickens

Positive modulation of gut microbiota in laying chickens may offer a strategy for reduction of Salmonella Typhimurium shedding and production of safer poultry products. In the current study, the caecal luminal microbiota of laying chicks was studied using 16S rRNA amplicon sequencing on DNA obtained from the chicks that were offered supplementation with commercial probiotics, synbiotics and/or Salmonella Typhimurium challenge. The load of Salmonella Typhimurium in various organs was quantified. Irrespective of the probiotics and synbiotics supplementation and Salmonella Typhimurium challenge, caecal microbiota was dominated by 22 distinct bacterial genera and 14 families that clustered into Actinobacteria, Proteobacteria and Firmicutes at phylum level. Taken together, probiotics and synbiotics supplementation increased (false discovery rate; FDR < 0.05) the abundance of Ruminococcus, Trabulsiella, Bifidobacterium, Holdemania and Oscillospira, indicating their role in maintaining gut health through lowering luminal pH and digestion of complex polysaccharides. Salmonella Typhimurium challenge decreased the abundance of Trabulsiella, Oscillospira, Holdemania, Coprococcus, Bifidobacterium and Lactobacillus and increased Klebsiella and Escherichia, indicating its role in caecal dysbiosis. Although probiotics and synbiotics supplementation positively modulated the caecal microbiota, they were not effective in significantly (P > 0.05) reducing Salmonella Typhimurium load in caecal tissue and invasion into vital organs such as liver and spleen. The early colonisation of laying chick caeca by probiotics and synbiotics had the potential to positively influence luminal microbiota; however, the microbial abundance and diversity were not sufficient to significantly reduce the shedding of Salmonella Typhimurium in faeces or invasion into internal organs during this study.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Organic Acids Modulate Systemic Metabolic Perturbation Caused by Salmonella Pullorum Challenge in Early-Stage Broilers

The objectives of this study were to determine the protective effects of organic acids (OA) in broilers exposed to Salmonella Pullorum challenge at early stage and to explore the potential benefits of OA by metabolomics analysis. The treatment groups included non-challenged, S. Pullorum-challenged, challenged group supplemented with virginiamycin, challenged group supplemented with OA in drinking water, challenged group supplemented with OA in feed, and challenged group supplemented with OA in combination in drinking water and feed. Results showed that early Salmonella challenge induced an acute systemic infection of broilers in the starter phase, followed by the grower phase without triggering clinical signs. OA supplementation promoted growth during the grower phase, and while OA in water contributed more, the positive effects of OA in combination were comparable to those of virginiamycin supplementation in challenged birds. Furthermore, OA could modulate the systemic metabolic perturbation caused by challenge as it alleviated stress responses mediated by steroid hormone, potentially attenuated antioxidant or immune defense, and modified intestinal microbiota metabolism. These results show a metabolic mechanism that may partly explain the potential benefits of OA in Salmonella challenged birds, and may contribute to the use of OA to control or reduce S. Pullorum infection in farm animals.