Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing

Effects of Feeding Fermented Cassava Leaves on Intestinal Morphology, Cecal Microbiota, and Metabolome in Hybrid Geese

In this study, we characterized the effects of a diet supplemented with fermented cassava leaves (FCLs) on growth performance, intestinal morphology, the cecal microbiota, and cecal metabolites in hybrid geese. We found that the FCL diet was beneficial to goose growth performance and also promoted a healthy intestinal morphology, as reflected by better morphology properties of the duodenum, jejunum, ileum, and cecum. Moreover, the FCL diet significantly altered cecal microbial diversity and composition, increasing the diversity and abundance of the beneficial Bacteroides. Further, the FCL diet increased the complexity and stability of cecal microbial co-occurrence network interactions as a result of altered topological distributions in the network, such as edges, density, degree, and betweenness. The FCL diet had clear impacts on the composition and abundance of cecal metabolites, with increases in metabolites involved in amino acid biosynthesis, digestion, and absorption, as well as an upregulation of associated metabolic pathways. Based on these benefits to growth performance, intestinal development, and cecal microbe-mediated metabolism in geese, FCLs can be utilized as a reliable feed resource for geese in tropical and subtropical regions.

Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata)

Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.

Melatonin feeding changed the microbial diversity and metabolism of the broiler cecum

To study the effect of melatonin supplementation on the gut microbes of broilers, 160 healthy 3-week-old Ross 308 broilers with similar body weights were selected and randomly divided into four groups (M0, M20, M40, and M80) supplemented with 0, 20, 40, or 80 mg/kg melatonin. The results showed that the abundance-based coverage estimator (ACE) index of cecum microorganisms was significantly lower in the M80 group. The dominant phyla of intestinal contents in the M0, M20, M40, and M80 groups were Bacteroidetes and Firmicutes. The M40 group showed an increase in the relative abundance of Bacteroidetes spp. in the intestine, while the relative abundance of Ruminococcus spp. in the intestine of the M20, M40, and M80 groups was significantly greater than that of the M0 group. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the supplementation of melatonin increases the expression of genes related to cellular processes (cell motility, cell growth and death, and cellular community-eukaryotes), environmental information processing (membrane transport and signal transduction), and genetic information processing (transport and transcription), and Cluster of Orthologous Groups (COG) of proteins functional analyses revealed that the supplementation of melatonin resulted in a significant increase in cellular processes and signaling (cell motility, signal transduction mechanisms, intracellular trafficking, secretion, and vesicular transport), information storage and processing (RNA processing and modification, chromatin structure and dynamics, translation, ribosomal structure, and biogenesis), metabolism (energy production and conversion, lipid transportation and metabolism, inorganic ion transport and metabolism, secondary metabolite biosynthesis, transport, and catabolism), and poorly characterized (general function prediction only). In summary, supplementation of feed with melatonin can increase the diversity of intestinal microorganisms and the relative abundance of Bacteroides and Firmicutes in the cecum, improve digestive ability and nutrient absorption ability, and positively regulate the metabolic ability of broilers.

Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese

1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.

Cassava Foliage Effects on Antioxidant Capacity, Growth, Immunity, and Ruminal Microbial Metabolism in Hainan Black Goats

Cassava (Manihot esculenta Crantz) foliage is a byproduct of cassava production characterized by high biomass and nutrient content. In this study, we investigated the effects of cassava foliage on antioxidant capacity, growth performance, and immunity status in goats, as well as rumen fermentation and microbial metabolism. Twenty-five Hainan black goats were randomly divided into five groups (n = 5 per group) and accepted five treatments: 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5) of the cassava foliage silage replaced king grass, respectively. The feeding experiment lasted for 70 d (including 10 d adaptation period and 60 d treatment period). Feeding a diet containing 50% cassava foliage resulted in beneficial effects for goat growth and health, as reflected by the higher average daily feed intake (ADFI), average daily gain (ADG) and better feed conversion rate (FCR), as well as by the reduced serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (CRE), and triglycerides (TG). Meanwhile, cassava foliage improved antioxidant activity by increasing the level of glutathion peroxidase (GSH-Px), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) and lowering malondialdehyde (MDA). Moreover, feeding cassava foliage was also beneficial to immunity status by enhancing complement 3 (C3), complement 4 (C4), immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin M (IgM). Furthermore, the addition of dietary cassava foliage also altered rumen fermentation, rumen bacterial community composition, and metabolism. The abundance of Butyrivibrio_2 and Prevotella_1 was elevated, as were the concentrations of beneficial metabolites such as butyric acid; there was a concomitant decline in metabolites that hindered nutrient metabolism and harmed host health. In summary, goats fed a diet containing 50% cassava foliage silage demonstrated a greater abundance of Butyrivibrio_2, which enhanced the production of butyric acid; these changes led to greater antioxidant capacity, growth performance, and immunity in the goats.

Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition

The present study aimed to investigate the impact of indoor and outdoor rearing systems on the biochemistry and microbial composition of White Roman geese, with a particular focus on the gut microbiome. Our results showed that geese reared in an outdoor system had significantly lower serum aspartate aminotransferase (AST) compared to those reared indoors, but lower levels of high-density lipoprotein (HDL) and higher levels of low-density lipoprotein (LDL). Moreover, the cecal microbiota of geese reared outdoors exhibited higher species evenness and increased alpha diversity, with a significant alteration in the F/B ratios. The bacterial taxonomy composition also differed between the 2 rearing systems, with higher relative abundances of the Firmicutes and Actinobacteria and lower relative abundances of the Bacteroidetes and Proteobacteria in the outdoor system. These findings suggest that rearing systems may play a critical role in shaping the gut microbiome and overall health of geese. Notably, our data demonstrated that indoor rearing was associated with a higher abundance of pathogenic genera and a lower abundance of commensal genera compared to outdoor rearing. Our study supports the hypothesis that rearing systems may alter the physiological functions and microbial composition of geese, and highlights the need for further research to confirm and expand upon these findings. In summary, our study underscores the importance of considering the impact of rearing systems on the gut microbiome and health of geese.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH₄⁺. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

The effect of combined dietary supplementation of herbal additives on carcass traits, meat quality, immunity and cecal microbiota composition in Hungarian white geese

The present study was performed to investigate the effects of dietary supplementation with herbal additives on meat quality, slaughter performance and the cecal microbial community in Hungarian white geese. A total of 60 newborn geese were assigned equally into the control group (CON) and the herbal complex supplemented group (HS). The dietary supplementations consisted of Compound Herbal Additive A (CHAA) including Pulsatilla, Gentian and Rhizoma coptidis, and Compound Herbal Additive B (CHAB) containing Codonopsis pilosula, Atractylodes, Poria cocos and Licorice. The geese in the HS group received a basal diet supplemented with 0.2% CHAA from day 0 to day 42 at the postnatal stage. Then from day 43 to day 70, the geese in HS group were provide a basal diet with 0.15% CHAB. The geese in the CON group were only provided with the basal diet. The results showed that the slaughter rate (SR), half chamber rates (HCR), eviscerated rate (ER) and breast muscle rate (BMR) in the HS group tended to increase slightly compared with the CON group (ns). In addition, the shear force, filtration rate and pH value of breast muscle and thigh muscle in the HS group were slightly enhanced compared to the CON group (ns). Significant increased levels in carbohydrate content, fat content and energy (P < 0.01) and significant decreased levels in cholesterol content (P < 0.01) were observed in the muscle of the HS group. The total amino acid (Glu, Lys, Thr and Asp) content in the muscle increased in HS group than in the CON group (P < 0.01). Dietary herb supplementations significantly increased the levels of IgG in serum (P < 0.05) on day 43 and higher levels of IgM, IgA and IgG (P < 0.01) were also observed in the HS group on day 70. Furthermore, 16S rRNA sequencing results indicated that herbal additives increased the growth of beneficial bacteria and inhibited the proliferation of harmful bacteria in the geese caecum. Altogether, these results offer crucial insights into the potential benefits of incorporating CHAA and CHAB into the diets of Hungarian white goose. The findings indicate that such supplementations could significantly improve meat quality, regulate the immune system and shape the intestinal microbiota composition.

Effects of Dietary Quinoa Seeds on Cecal Microorganisms and Muscle Fatty Acids of Female Luhua Chickens

To study the effects of adding quinoa seed (raw grain) to the diet of the Luhua chicken on the cecal microorganism abundance and fatty acid composition of muscle, 120 49-day-old healthy female dewormed Luhua chickens (body weight 1476.21 ± 101.39 g) were randomly divided into 4 groups, with 3 replicates in each group and 10 chickens in each repetition. The control group (CK group) was fed a basal diet and the experimental groups were fed with 4% (Q4), 8% (Q8), and 12% (Q12) quinoa seed (raw grain) added to the basal diet for 75 days. After 121 days of age, the animals were slaughtered and the 16S rRNA characteristics of cecal flora, as well as composition and content of fatty acids in muscle, were determined and analyzed. The content of unsaturated fatty acids (UFAs), docosahexaenoic acid (C22:6n3; DHA) and n-3 polyunsaturated fatty acids (n-3 PUFAs) in the breast and leg muscles significantly increased in the experimental groups supplemented with quinoa seeds (p < 0.05). However, the content of saturated fatty acids (SAFs) and ratio of n-6/n-3 in breast muscle and leg muscle significantly decreased (p < 0.05). In addition, adding a certain percentage of quinoa seeds in the diet can also affect the community composition and content of microorganisms in the ceca of Luhua chickens. At the phylum level, the Proteobacteria, Actinobacteria, Synergistetes and Melainabacteria in experimental groups (Q4, Q8 and Q12) were significantly lower than those in the CK group (p < 0.05). At the genus level, Desulfovibrio, Synergistes, Olsenella, Parabacteroides, Mailhella, Sutterella and Ruminiclostridiu in group Q4 were significantly lower than those in group CK (p < 0.05) while Faecalibacterium in Q8 group, and Lawsonia and Faecalibacterium in Q12 group were significantly higher than those in the CK group (p < 0.05). Enrichment analysis of the microbial function showed that compared with the CK group, Metabolism and Enzyme Families were significantly enriched in the Q4 group (p < 0.05). Cellular Processes and Signaling were significantly enriched in the Q8 group (p < 0.05). The association analysis of fatty acids with microorganisms showed that the abundance of Faecalibacterium, Lawsonia and Meagmonas was significantly correlated with partial SFAs and UFAs (p < 0.05). In conclusion, adding quinoa seeds to diets significantly increased the content of muscle DHA, UFAs and n-3 PUFAs. The content of SAFs and the n-6/n-3 ratio were significantly reduced. Taken together, quinoa can effectively improve the cecal microbiota structure, inhibit the number of harmful bacteria and increase the number of beneficial bacteria, regulating the intestinal environment and promoting the body health of female Luhua chickens.

Effects of Dietary Oregano Essential Oil on Cecal Microorganisms and Muscle Fatty Acids of Luhua Chickens

This experiment was conducted to investigate the effects of oregano essential oil on the cecal microorganisms and muscle fatty acids of Luhua chickens. One hundred and twenty 49-day-old healthy dewormed Luhua chickens were randomly divided into four groups with three replicates per group and ten chickens per replicate. The corn−quinoa and soybean meal diets were supplemented with 0 (Q8 group), 50 (QO50 group), 100 (QO100 group) and 150 mg·kg−1 (QO150 group) of oregano essential oil, respectively, and the experiment lasted for 75 days. The composition of intestinal flora was detected by Illumina sequencing of the 16S rRNA V4 region, and the composition and content of fatty acids in the muscles were analyzed by gas chromatography. The results showed that dietary oregano essential oil can effectively increase the contents of elaidic acid (C18:ln9t), polyunsaturated fatty acids (PUFAs) and n-3 polyunsaturated fatty acids (n-3 PUFAs) in breast muscle tissues. However, the fatty acid composition and PUFA content in leg muscle tissues were not significantly improved. According to a 16S rRNA high-throughput sequencing analysis, dietary oregano essential oil supplementation with a certain concentration can change the cecal microbial community composition of broilers. At the phylum level, Elusimicrobia in the QO150 group was significantly lower than that in Q8 group (p < 0.05). At the genus level, Phascolarctobacterium, Parasutterella and Bilophila in the experimental groups (QO50, QO100 and QO150) were significantly lower than those in the Q8 group (p < 0.05). An enrichment analysis of the microbial function found that the amino acid metabolism, energy metabolism, metabolism, signal transduction and genetic information processing were mainly enriched in the experimental groups, which promoted the digestion and absorption of nutrients and enhanced intestinal barrier functioning. An analysis of the association between fatty acids and microbes found that the abundance of microbiota was significantly correlated with partially saturated fatty acids (SFAs) and unsaturated fatty acids (UFAs) (p < 0.05). In conclusion, the dietary addition of oregano essential oil can effectively improve cecal microbial community composition, promote the digestion and absorption of nutrients, and enhance intestinal barrier functioning. It can significantly improve the content of some fatty acids, and there was a certain correlation between caecum microorganisms and fatty acid deposition in muscles.

Co-fermented yellow wine lees by Bacillus subtilis and Enterococcus faecium regulates growth performance and gut microbiota in finishing pigs

Fermented yellow wine lees (FYWL) are widely used to increase feed utilization and improve pig performance. Based on the preparation of co-FYWL using Bacillus subtilis and Enterococcus faecalis, the purpose of this study was to investigate the effects of co-FYWL on growth performance, gut microbiota, meat quality, and immune status of finishing pigs. 75 pigs were randomized to 3 treatments (5 replicates/treatment), basal diet (Control), a basal diet supplemented with 4%FYWL, and a basal diet supplemented with 8%FYWL, for 50 days each. Results showed that the 8% FYWL group significantly reduced the F/G and increased the average daily weight gain of pigs compared to the control group. In addition, 8% FYWL improved the richness of Lactobacillus and B. subtilis in the gut, which correlated with growth performance, serum immune parameters, and meat quality. Furthermore, acetate and butyrate in the feces were improved in the FYWL group. Simultaneously, FYWL improved the volatile flavor substances of meat, increased the content of flavor amino acids, and played a positive role in the palatability of meat. In addition, FYWL increased serum IgA, IgM, IL-4 and IL-10 levels. Overall, the growth performance, the gut microbiota associated with fiber degradation, meat quality, and immune status were improved in the 8% FYWL group.

Effects of maize silage feeding on growth performance, carcass characteristics, digestive system length, chemical composition, and meat quality of domestic geese

This study aimed to explore the effects of corn silage (CS) on growth performance, carcass characteristics, digestive system length, and some meat quality traits of geese. A total of 35 19-week-old Turkish indigenous male geese with similar body weight were randomly divided into five groups with individual pens of seven geese per group and fed for 84 D. The treatments were composed of a basal diet (100% concentrate feed) without corn silage (0CS), 10% CS + 90% concentrate feed (10CS), 20% corn silage + 80% concentrate feed (20CS), 30% corn silage + 70% concentrate feed (30CS), and 40% corn silage + 60% concentrate feed (40CS). Dietary CS supplementation did not affect growth performance, dressing percentage, liver and gizzard weights, digestive system length of geese, and the organoleptic quality characteristics of meat. The 0CS and 20CS geese had a higher instrumental hardness value than other treatment geese (p < 0.05). Also, the 40CS group had the lowest hardness value (p < 0.05). Adhesiveness value was lower in the 0CS group compared to all silage treatments (p < 0.05). Gumminess value was lower in the 40CS group compared to the control group (p < 0.05). The 10CS treatment reduced the L value of thigh and breast meat compared with those of the other treatments (p < 0.05). The a and b color values and pH values of breast and thigh meats were not affected by dietary CS supplementation (p > 0.05). Fat content of the meat decreased in the 30CS treatment compared to 0CS (p < 0.05). The results of the present study suggest that corn silage could be used up to 40% in the Turkish goose variety diet, without affecting the performance and meat quality, and thus, geese can be produced more economically.

Comparative Analyses of Production Performance, Meat Quality, and Gut Microbial Composition between Two Chinese Goose Breeds

Simple Summary

Poultry is one of the most frequently consumed meats in the world and plays an important role in the daily life of people. Goose meat is consumed by consumers because it contains a relatively high proportion of polyunsaturated fatty acids. Meat quality traits, production performance, and cecal microbiota diversity in two goose breeds (Zi goose and Xianghai flying goose) were evaluated in this study. Understanding these aspects not only provides a reference for the exploration of the relationship between the cecal microbiota and production performance but also guidelines for the human consumption of healthy poultry meat.

Abstract

Goose meat is consumed by consumers because it contains a relatively high proportion of polyunsaturated fatty acids (PUFAs). This study was conducted to explore the main differences in production performance, breast meat quality traits, and cecal microbiota compositions between the Zi goose (ZG) and Xianghai flying goose (FG). The production performance and breast meat quality trait analyses showed that compared with the ZG, the FG had a higher right breast muscle index, ileum villi height/crypt depth ratio (VH/CD), and cecum fermentation rate (higher short-chain fatty acid (SFCA) concentration); a lower abdominal fat index; a higher proportion of PUFAs; and a lower shear force. Spearman’s correlation coefficients between the cecal microbiota composition and production performance indexes suggested that the genus Faecalibacterium was positively associated with production performance; in contrast, the genus Candidatus Saccharimonas was negatively correlated with production performance; moreover, the Ruminococcus torques group, Parasutterella, and Methanobrevibacter were negatively related to the VH/CD. Taken together, in this particular trial, FG had better production performance, healthier meat quality traits, and better intestinal digestion and absorption capacities than ZG. These results not only provide a useful data reference for the production of healthy geese for human consumption but can also help guide the utilization of goose breed resources.

Effects of Sucrose, Glucose and Molasses on Fermentation Quality and Bacterial Community of Stylo Silage

To better understand the mechanism underlying water-soluble carbohydrates (WSC)-regulated silage fermentation, the bacterial community and fermentation quality of stylo (Stylosanthes guianensis) ensiled without (sterile distilled water) (CK) or with 10 g/kg sucrose (S), 10 g/kg glucose (G), and 10 g/kg molasses (M) were investigated. Each treatment was ensiled in three plastic bag silos for 30 days. The DM of stylo was 301.0 g/kg (fresh matter basis), while the contents of CP, WSC, NDF and ADF were 104.9, 12.3, 510.4 and 407.6 g/kg (dry matter basis), respectively. The bacterial community was characterized by using 16Sr DNA sequencing technology. The addition of WSC significantly altered both fermentation quality and the bacterial community of stylo silage. The additive treatment resulted in higher lactic acid (17.2 vs. 67.0 g/kgDM), lower pH (4.68 vs. 4.46), and lower acetic acid (37.0 vs. 28.9 g/kgDM) compared with the control. In addition, no propionic acid and butyric acid were detected in the additive treatment groups. These results indicated that WSC additives helped to produce greater quality stylo silage. Meanwhile, the Shannon index was higher, and the Simpson index was lower in the WSC additive-treated groups compared with the control, indicating that WSC improved microbial diversity. Furthermore, WSC treatments increased the abundance of acid-producing bacteria Megamonas and Bacteroides, decreased the abundance of Weissella, and inhibited the growth of the undesirable Enterobacter. Our results confirmed that sucrose, glucose and molasses have similar beneficial effects on both bacterial community and silage fermentation of stylo. Molasses was recommended to be used in stylo silage for economic benefit and resource utilization.

Effect of lactic acid bacteria, molasses, and their combination on the fermentation quality and bacterial community of cassava foliage silage

This study investigated the effects of LAB inoculants (L) and molasses (M) on the microbial community and fermentation quality of cassava foliage (CF). The small segments (about 2-3 cm) CF were ensiled in plastic bags and incubated at normal temperature (25°C). Four treatments were carried out as follows: control (no additives, CK), LAB inoculants (Lactobacillus plantarum, L), molasses (M), and LAB in combination with molasses (LM). The LAB and molasses obviously altered the bacterial community structure of the CF silage and enhanced the fermentation quality. The combination addition could increase the abundance of Lactobacillus and reduce the Pseudomonas. The LAB and molasses also significantly elevated the lactic acid concentration (P < 0.001) and decreased the pH (P < 0.001), as well as the concentrations of acetic acid, propionic acid, butyric acid, and ammonia-N (P < 0.05). In addition, the combination treatment displayed more effective results on silage fermentation. The LAB and molasses improved the fermentation quality of the CF silage by altering the bacterial community structure. Furthermore, the bacterial community was significantly correlated with fermentation indexes.

Natural Fermentation Quality and Bacterial Community of 12 Pennisetum sinese Varieties in Southern China

This study investigated the fermentation quality of 12 varieties of Pennisetum sinese grown in different regions of Southern China. Following the production of silage from the natural fermentation of P. sinese, the interplay between the chemical composition, fermentation characteristics, environmental factors, and microbiome was examined to understand the influence of these factors on the fermentation quality of silage. The silage quality produced by most of the P. sinese was low; the pH value of the silage was high (4.26–4.86), whilst the lactic acid content was low (10.7–24.1 g/kg DM), with V-scores between 57.9 and 78.3. The bacterial alpha diversities of the 12 P. sinese silages were distinct. There was a predominance of undesirable bacteria (Pseudomonas, Massilia, and Raoultella), which likely caused the poor fermentation quality. The chemical composition and fermentation characteristics of the silage were closely correlated with the composition of the bacterial community. Furthermore, environmental factors (precipitation, temperature, humidity, location) were found to significantly influence the microbiome of the silage. The results confirmed that silage produced from the natural fermentation of 12 different P. sinese varieties had significant variation in their bacterial communities. The difference in environmental factors, due to the P. sinese being grown in various locations across south china, greatly affected the bacterial community found in the silage and thus the fermentation quality. The specific cultivar used for the silage and the environment in which the cultivar is grown must therefore be considered before the initiation of production of silage in order to ensure a higher quality product.

Effects of king grass and sugarcane top in the absence or presence of exogenous enzymes on the growth performance and rumen microbiota diversity of goats

In the present study, the feasibility of sugarcane top (ST) application in the goat's diet was evaluated. A total of 20 goats were randomly divided into four groups. The dietary treatments were set as follows: animals were fed with king grass (KG), KG with exogenous enzymes (KGE), ST, and ST with exogenous enzymes (STE). The animals were given free access to feed and water. After 15 days of adaptation and 60 days of the experiment, the growth performance, plasma parameters, and rumen microbiota of goats were assessed. The results showed that the KG, ST, and exogenous enzyme supplement had no significant effects on the growth performance and plasma parameters. The diet affected the rumen microbiota diversity and structure, and the alpha and beta diversity in the animals fed with ST were dramatically greater compared with the animals fed with KG. The abundances of Proteobacteria, Cyanobacteria, and Elusimicrobia were significantly decreased in the animals fed with KG or KGE, while the abundances of Firmicutes and Euryarchaeota were significantly higher in the animals fed with KG or KGE. Furthermore, the microbial communities were also different at the genus level. Moreover, the exogenous enzymes had a slight effect on rumen microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the greatest differences were found in bacterial taxa, and these specific taxa could be used as biomarkers to distinguish rumen microbiota. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional profile prediction indicated that the dietary treatments of ST and KG could also alter the gene expression pattern in nutrient and energy metabolism, as well as replication and repair of genetic information pathways. Collectively, the dietary treatments of KG and ST in the absence or presence of exogenous enzymes had similar effects on the growth performance and plasma parameters of goats. Besides, the KG and ST diets could affect the rumen microbiota community and function of goats. Therefore, ST could be used as a promising alternative feed resource for ruminants without the addition of exogenous enzymes in tropical regions.

Impacts of Citric Acid and Malic Acid on Fermentation Quality and Bacterial Community of Cassava Foliage Silage

The microbiota and fermentation quality of cassava foliage (CF) ensiled in the absence of additive (CK), or the presence of citric acid (CA), malic acid (MA), and their combination with a Lactobacillus plantarum strain (CAL and MAL)were investigated. These additives reduced (P < 0.05) the pH, butyric acid, and ammonia-N contents but increased (P < 0.05) the lactic acid content, and CAL and MAL showed similar remarkable effects. Paenibacillus (mean, 27.81%) and Bacillus (mean, 16.04%) were the predominant strains in CF silage. The addition of CA or MAL increased the abundance of Paenibacillus (25.81–52.28% and 47.97%, respectively), and the addition of MA increased the abundance of Bacillus (15.76–32.48%) compared with the CK group. Moreover, CAL and MAL increased the abundances of the potentially desirable bacteria Cellulosimicrobium (CAL 0–12.73%), Hyphomicrobium (0–7.90% and 8.94%), and Oceanobacillus (0–8.37% and 3.08%) compared with the CK group. These findings suggested that CA and MA could enhance the silage quality of CF, and their combinations with Lactobacillus plantarum were more effective.

Fermented Feed Supplement Relieves Caecal Microbiota Dysbiosis and Kidney Injury Caused by High-Protein Diet in the Development of Gosling Gout

Firstly, forty-eight 1-day-old goslings were randomly allocated to four groups and were fed diets containing crude protein (CP) at different concentrations: 160, 180, 200, and 220 g/kg in Experiment One. We found a dose-dependent relationship between the dietary protein levels and morbidity of gosling gout. The concentration of serum uric acid (UA), creatinine (Cr), and urea nitrogen (UN), and the activity of xanthine oxidase in the 220CP groups were significantly higher than those in the low-protein diet groups. Beneficial microbes, including Akkermansia, Lactococcus, and Butyricicoccus were enriched in the ceca of healthy goslings, while the microbes Enterococcus, Enterobacteriaceae, and Bacteroides were enriched in those with gout. Then, we explored the effects of fermented feed on gosling gout caused by high-protein diets in Experiment Two. A total of 720 1-day-old goslings were randomly allotted to four experimental groups: CN (162.9 g/kg CP), CNF (167.5 g/kg CP, replacing 50 g/kg of the basal diet with fermented feed), HP (229.7 g/kg CP, a high-protein diet), and HPF (230.7 g/kg CP, replacing 50 g/kg of the high-protein diet with fermented feed). We found that the cumulative incidence of gout increased in the HP group compared with that in the control, but decreased in the HPF group compared to that in the HP group. Similarly, the concentration of serum UA in the HP group was higher than that in the CN group, but decreased in the HPF group. Meanwhile, compared with the HP group, using fermented feed in diets decreased the abundance of Enterococcus in the ceca of goslings, while increasing the abundance of Lactobacillus. These results suggest that appropriate dietary protein levels and the fermented feed supplement might relieve the kidney injury and gut microbiota dysbiosis caused by high-protein diets in the development of gosling gout.

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing

There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.

Biogeography of microbiome and short-chain fatty acids in the gastrointestinal tract of duck

It is generally accepted that domestic ducks are valuable protein sources for humans. The gastrointestinal ecosystem contains enormous and complicated microbes that have a profound effect on the nutrition, immunity, health, and production of domestic ducks. To deeply understand the gastrointestinal microbial composition of domestic ducks, we investigated the microbiomes of 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) and the short-chain fatty acids in 15 healthy muscovy ducks based on 16S rRNA gene sequencing, qPCR, and gas chromatography. As a result, 1 029 735 sequences were identified into 35 phyla and 359 genera. Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, with Bacteroidetes being most abundant in the cecum. The population of the total bacteria and the representatives of the Firmicutes, Bacteroidetes, and Bacteroides groups increased from the proximal to the distal part of the GIT. Bacteroides was the most dominant group in the cecum. Acetate, propionate, and butytrate, as well as gene copies of butyryl-CoA including acetate-CoA transferase and butyrate kinase, were significantly higher in cecum than in other sections. Isobutyrate, valerate, and isovalerate were only found in the cecum. The differences of microbial composition and the short-chain fatty acids of their metabolites among these 7 intestinal locations might be correlated with differences in gut function. All these results provide a reference for the duck gastrointestinal microbiome and a foundation for understanding the types of bacteria that promote health and enhance growth performance and decrease instances of disease in duck breeding.

Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing

During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.

Silage fermentation and ruminal degradation of cassava foliage prepared with microbial additive

To effectively utilize the tropical cassava (Manihot esculenta Crantz) foliage (CF) resources, the CF silages were prepared with microbial additives, including Chikuso-1 (CH1, Lactobacillus plantarum), Snow Lact L (SN, L. rhamnosus), Acremonium cellulase (CE), SN + CE and CH1 + CE. Silage fermentation, chemical composition and ruminal degradation were studied in Hainan, China. CF silages prepared with lactic acid bacteria (LAB) and CE were well preserved, with a higher (P < 0.05) lactic acid, a lower (P < 0.05) pH value, butyric acid content and NH3-N ⁄ total-N compared with the controls. The additive-treated silages showed increased crude protein (CP) content, but decreased (P < 0.05) NDF and ADF contents. Meanwhile, the additive treatment improved relative feed value and ruminal degradability of dry matter (DM), CP, neutral detergent fiber and acid detergent fiber. In addition, the combination of LAB and CE resulted in better fermentation quality and ruminal degradability compared with LAB or CE single treatment. The results demonstrated that the CF could be prepared as ruminant feed, and the combination of LAB and CE might exert beneficial synergistic effect on silage fermentation.

Comparative Analysis of the Gut Microbial Composition and Meat Flavor of Two Chicken Breeds in Different Rearing Patterns

The objective of the study is to compare the effects of free-range (FR) and cage-range (CR) breeding on gut microbiota and flavor compounds of Caoke (C) and Partridge Shank chickens (Q). A total of 120 experimental chickens were assigned to FR group and CR group; each group contain both 30 Caoke chickens and 30 Partridge Shank chickens. At 154 d old, 12 chickens of each group were selected and their cecal contents were extracted and examined for the composition of gut microbiota by illumina sequencing of the V3 region of the 16S rDNA genes, and flavor compounds were analyzed through headspace-solid-phase microextraction (HS-SPME) method. The results showed that, except for acids, the amount of flavor substances in the FR group was higher than those in the CR group, especially the content of Hexanal and D-limonene. Meanwhile, the higher concentrations of carbonyls including (E,E)-2,4-decadienal, (E)-2-decenal, (E)-2-octenal, and pentanal were in the FR chicken meat, but the differences in concentrations compared with CR were not significant. High levels of ethyl hexanoate and β-ocimene were only detected in FR groups. The Firmicutes had the highest proportion of chicken cecal microbiota, whereas the Fusobacteria was only detected in the cecal samples of Q chicken in FR group. Actinobacteria was more prevalent in FR groups than in CR groups. Meanwhile, in Q chickens, the proportions of Bacteroidetes and Proteobacteria in FR group were higher than those in CR group. Using MG-RAST Subsystem Technology, we found that some genes were associated with the formation of precursors of flavor compounds or with the metabolism and degradation of aromatic compounds. Overall, CR and FR breeding influenced the gut microbiota and flavor compounds, potentially because of the changes in diet and living conditions.

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose

Goose is an economically important herbivore waterfowl supplying nutritious meat and eggs, high-quality liver fat, and feathers. However, biogeograhpy of the gut microbiome of goose remains limited. The aim of this study was to investigate the microbiota inhabiting 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) of 180-day-old geese and the short-chain fatty acids (SCFA) of their metabolites based on 16S rRNA gene sequences and gas chromatography, respectively. Consequently, 3,886,340 sequences were identified into 29 phyla and 359 genera. Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, in which Bacteroidetes (28%) and Fusobacteria (0.8%) in the cecum were significantly higher than those in other sections (∼4.4 and 0.1%, respectively). In addition, Cyanobacteria in the gizzard (4.9%) was significantly higher than those in other gut sections except the proventriculus (2.4%). At the genus level, Bacteroides was the most dominant group in the cecum at 23.7%, which was much more than those in the 6 other sections (less than 4.6%). Moreover, Faecalibacterium and Butyricicoccus were significantly high in the cecum (P < 0.05). Results of SCFA showed that acetic and butyric acids in the cecum were significantly higher than those in the 6 other sections (P < 0.05); this result was consistent with the high abundance of Bacteroides, Faecalibacterium, Prevotella, and Butyricicoccus in the cecum. Additionally, isobutyric, isovaleric, and valeric acids were found only in the cecum. The different microbial compositions among the 7 gastrointestinal locations might be a cause and consequence of gut functional differences. All these results could offer some information for future study of the relationship between gastrointestinal microbiota and the ability of fiber utilization and adaptability.

The optimization of fermentation conditions for producing cellulase of Bacillus amyloliquefaciens and its application to goose feed

The proper culture conditions for producing cellulase of Bacillus amyloliquefaciens S1, isolated from the cecum of goose was optimized by single-factor experiment combined with orthogonal test. The properties of the cellulase were investigated by DNS method. The appropriate doses of B. amyloliquefaciens S1 were obtained by adding them to goose feed. It indicated that the suitable culture conditions of producing cellulase were the culture temperature of 37°C, the initial pH of 7.0, the incubation time of 72 h and the loaded liquid volume of 75 ml per 250 ml. The effects of each factor on producing cellulase by B. amyloliquefaciens S1 were as follows: initial pH > incubation time = culture temperature > loaded liquid volume. The optimum reaction temperature and pH were 50°C and 7.0, respectively. This enzyme is a kind of neutral cellulase that possesses resistance to heat and acidity. It showed high activity to absorbent cotton, soya bean meal and filter paper. By adding different doses of B. amyloliquefaciens S1 to the goose feed, it was found that the egg production, average egg weight, fertilization rate and the hatching rate were promoted both in experiment 1 (1.5 g kg-1) and experiment 2 (3 g kg-1). Also the difference of egg production, fertilization rate and hatching rate between experiment 1 and control group was obvious (p < 0.05), and the average egg weight was significantly increased in experiment 2 (p < 0.05).

Effect of probiotics on the meat flavour and gut microbiota of chicken

To date, no report has demonstrated the use of beneficial microbes for contributing to the flavour characteristics and gut microbiota diversity of chicken. Here, we selected six probiotics obtained from our laboratory and supplemented them in six different combinations to 420 newborn male Qingjiaoma chickens under the same controlled living environment (60 birds, no probiotic supplements). The results showed that chicken supplemented with Bacillus species showed beneficial effects in body weight. Acetate is the major fermentation production in the chicken caecum, and chicken supplemented with Pediococcus pentosaceus had the average higher short chain fatty acids (SCFAs) contents. In chicken caecal microflora, the abundance of Bacteroidetes bacteria was positively correlated with the content of propionate, butyrate, and isobutyrate, whereas an increase in acetate content was positively correlated to the abundance of Firmicutes. Compared to chickens without probiotic supplement, chickens supplemented with P. pentosaceus had more characteristic flavour compounds in the sampled breast meat, especially higher concentrations of (E)-2-heptenal, (E,E)-2,4-nonadienal, and certain C6-C9 unsaturated fatty acids. This resulted in a stronger chicken-fatty or fatty odour which directly improved the flavour. These findings suggest that probiotics can improve chicken meat flavour and increase gut microbiota diversity.