Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing

Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese

It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days), Clostridia_UCG-014, RF39 (at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.IMPORTANCELow dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.

Identification and characterization of multiple novel picornaviruses in fecal samples of bar-headed goose

Introduction

The bar-headed goose (Anser indicus), one of the most well-known high-altitude birds, is renowned for its adaptation to high-altitude environments. Previous studies have shown that they can be infected with highly pathogenic avian influenza; however, there is currently limited research on other viruses in bar-headed geese.

Methods

In this study, 10 fecal samples of healthy bar-headed geese were collected, and viral metagenomics method was conducted to identify novel picornaviruses.

Results

Seven novel picornaviruses were identified in the fecal samples of bar-headed geese. Most of these picornaviruses were genetically different from other currently known viruses in the NCBI dataset. Among them, PICV4 was determined to be a new species belonging to the Anativirus genus, PICV5 and PICV13 were classified as novel species belonging to the Hepatovirus genus, and the remaining four picornaviruses (PICV1, PICV19, PICV21, and PICV22) were identified as part of the Megrivirus A species of the Megrivirus genus. Recombinant analysis indicates that PICV21 was a potential recombinant, and the major and minor parents were PICV1 and PICV22, respectively.

Conclusion

The findings of this study increase our understanding of the diversity of picornaviruses in bar-headed geese and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species.

Alteration of the gut microbial composition of critically endangered Malayan tigers (Panthera tigris jacksoni) in captivity during enrichment phase

BACKGROUND

Enrichment activities may influence the microbiomes of captive tigers', affecting their health, digestion, and behavior. Currently, there are few studies that address the impact of enrichment activity on tigers' health. This study aimed to determine the diversity of the gut microbiome in captive Malayan tigers at Zoo Melaka and Night Safari during the environmental enrichment phase using a metabarcoding approach.

METHODS AND RESULTS

This study utilized different enrichment activities which catered for food, sensory, and cognitive enrichment. Eleven fresh fecal samples from captive Malayan tigers at Zoo Melaka and Night Safari were collected under different conditions. All samples were extracted and 16S rRNA V3-V4 region amplicon sequencing was used to characterize the gut microbiome of captive Malayan tigers subjected to various enrichment activities. Firmicutes, Actinobacteriota, and Fusobacteriota were the dominant phyla observed in the gut microbiome of captive Malayan tigers during enrichment activities. This study revealed β-diversity significantly varied between normal and enrichment phase, however no significant differences were observed in α-diversity. This study demonstrates that environmental enrichment improves the gut microbiome of Malayan tigers because gut microbes such as Lachnoclostridium, which has anti-inflammatory effects and helps maintain homeostasis, and Romboutsia, which has a probiotic effect on the gut microbiome.

CONCLUSIONS

This study provides valuable insights into the effects of enrichment activities on the gut microbiome of captive Malayan tigers, offering guidance for enhancing captive management practices aimed at promoting the health and well-being of Malayan tiger in captivity.

Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes (Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China

The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose

Introduction

Gut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function.

Methods

In order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota.

Results

The results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food.

Conclusion

The host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

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.

Comparison of the Gut Microbial Communities of Domestic and Wild Mallards (Anas platyrhynchos) Based on High-Throughput Sequencing Technology

Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

The Prophylactic Protection of Salmonella Typhimurium Infection by Lentilactobacillus buchneri GX0328-6 in Mice

Salmonellosis is a disease caused by non-typhoid Salmonella, and although some lactic acid bacteria strains have been shown previously to relieve Salmonellosis symptoms, little has been studied about the preventive mechanism of Lentilactobacillus buchneri (L. buchneri) against Salmonella infection in vivo. Therefore, the L. buchneri was fed to C57BL/6 mice for 10 days to build a protective system of mice to study its prevention and possible mechanisms. The results showed that L. buchneri GX0328-6 alleviated symptoms caused by Salmonella typhimurium infection among C57BL/6 mice, including low survival rate, weight loss, increase in immune organ index and hepatosplenomegaly, and modulated serum immunoglobulin levels and intrinsic immunity. Importantly, the L. buchneri GX0328-6 enhanced the mucosal barrier of the mouse jejunum by upregulating the expression of tight junction proteins such as ZO-1, occludins, and claudins-4 and improved absorptive capacity by increasing the length of mouse jejunal villus and the ratio of villus length to crypt depth and decreasing the crypt depth. L. buchneri GX0328-6 reduced the intestinal proliferation and invasion of Salmonella typhimurium by modulating the expression of antimicrobial peptides in the intestinal tract of mice, and reduced intestinal inflammation and systemic spread in mice by downregulating the expression of IL-6 and promoting the expression of IL-10. Furthermore, L. buchneri GX0328-6 increased the relative abundance of beneficial bacteria colonies and decreased the relative abundance of harmful bacteria in the cecum microflora by modulating the microflora in the cecum contents.

Synergistic mediating effect of edible fungal polysaccharides (Auricularia and Tremellan) and Crataegus flavonoids in hyperlipidemic rats

Both edible fungal polysaccharides (Auricularia and Tremellan) and Crataegus flavonoids promote the balance of dyslipidemia, which have a positive biological regulating effect on intestinal flora. In this study, the extraction of water-soluble polysaccharides from Auricularia and Tremellan was investigated and optimized firstly. Polysaccharides and flavonoids were then combined to study the effects on the mediating role of abnormal blood lipid concentration and intestinal flora in vivo. The rats were divided into 10 groups, the NC (normal control), HM (model), PCI (Simvastatin control), PCII (Fenofibrate control), AAP (Auricularia auricular Polysaccharide), TFP (Tremella fuciformis Polysaccharide), HF (Crataegus Flavonoid), LDC (Low-dose combination), MDC (Medium dose combination), and HDC (High-dose combination), used to explore the impact of polysaccharides and flavonoids complex on state of blood lipid, liver, and intestinal flora of dyslipidemia rats. The results showed that the combination of polysaccharides and flavonoids could significantly decrease the levels of triglyceride (TG), total cholesterol (TC), low-density lipoprotein (LDL-C), and increase the level of high-density lipoprotein cholesterol (HDL-C). It also significantly decreased the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and improved liver morphology. What is more, the HDC favorably alters the intestinal microflora balance, promotes intestinal integrity and mobility, and inhibits the growth of harmful bacteria such as Escherichia coli/Shigella and Clostridium compared with HM group. In brief, the combination of polysaccharides and flavonoids had a synergistic effect on the remission of dyslipidemia, and promoted health by improving lipid metabolism, protecting liver tissue, and regulating the intestinal flora in hyperlipidemia rats.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis

Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.

First Report of Fecal Microflora of Wild Bar-Headed Goose in Tibet Plateau

The bar-headed goose (Anser indicus) has two black spots on its head. It is considered an important bird in China. It breeds in plateau lakes, especially saltwater lakes, and swamp areas. However, the intestinal flora of wild bar-headed geese in the Tibet Autonomous Region is currently not known. In this study, 16S rDNA sequencing was performed on the intestinal microbes of wild bar-headed geese. A total of 513,505 reads of raw data were obtained, and the results analyzed the average number of 128,376 ± 2,392 reads per sample. The microbiota of all samples consists of 10 main bacterial phyla, including Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Patescibacteria, Deferribacteres, Planctomy-cetes, Fusobacteria, and Tenericutes. The results indicated that Firmicutes (67.34%) was the predominant phylum, followed by Proteobacteria (29.03%) and Cyanobacteria (1.97%). In our research, we identified the intestinal flora of the wild bar-headed goose, which provides valuable information for further research on the gene function of the bar-headed goose and the intestinal flora of wild animals. These findings are also useful and valuable for genetic and high-altitude research in the Tibet Autonomous Region.

Effect of Fluoride in Drinking Water on Fecal Microbial Community in Rats

Intestinal nutrition has a close association with the onset and development of fluorosis. Intestinal microbes play a major role in intestinal nutrition. However, the effect of fluoride on intestinal microbes is still not fully understood. This study aimed to evaluate the dose-response of fluoride on fecal microbes as well as the link between fluorosis and fecal microbes. The results showed that fluoride did not significantly alter the diversity of fecal microbiota, but richness estimators (ACE and Chao) increased first, and then decreased with the increase of water fluoride. At the genus level, 150 mg/L fluoride significantly reduced the abundances of Roseburia and Clostridium sensu stricto, and 100 mg/L and 150 mg/L fluoride obviously increased the abundances of Unclassified Ruminococcaceaes and Unclassified Bdellovibrionales, respectively. The correlation analysis showed fluoride exposure had a negative association with Roseburia and Turicibacter and was positively associated with Pelagibacterium, Unclassified Ruminococcaceae, and Unclassified Bdellovibrionales. Dental fluorosis was negatively associated with Clostridium sensu stricto, Roseburia, Turicibacter, and Paenalcaligenes and had a positive association with Pelagibacterium, Unclassified Ruminococcaceae, and Unclassified Bdellovibrionales. In conclusion, this study firstly reports fluoride in drinking water has a remarkable biphasic effect on fecal microbiota in rats, and some bacteria are significantly associated with fluoride exposure and dental fluorosis. These results indicate the gut microbiota may play an important role in fluorosis, and some bacteria are likely to be developed as biomarkers for fluorosis.

Seasonal Changes in the Distinct Taxonomy and Function of the Gut Microbiota in the Wild Ground Squirrel (Spermophilus dauricus)

Seasonal breeding is a normal phenomenon in which animals adapt to natural selection and reproduce only in specific seasons. Large studies have reported that the gut microbiota is closely related to reproduction. The purpose of this study was to explore the distinct taxonomy and function of the gut microbiota in the breeding and non-breeding seasons of the wild ground squirrel (Spermophilus dauricus). The 16S rRNA gene sequencing technology was utilized to sequence the gut microbiota of the wild ground squirrel. PICRUSt analysis was also applied to predict the function of the gut microbiota. The results suggested that the main components of the gut microbiota in all samples were Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between the breeding and non-breeding seasons. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were more abundant in the non-breeding season, while Blautia and Streptococcus were more abundant in the breeding season. The results of a functional prediction suggested that the relative abundance of functional categories that were related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism increased in the breeding season. The relative abundance of energy metabolism, transcription, and signal transduction increased in the non-breeding season. Overall, this study found differences in the taxonomy and function of the gut microbiota of the wild ground squirrel between the breeding and non-breeding seasons, and laid the foundation for further studies on the relationship between the gut microbiota and seasonal breeding.

Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau

Microbial communities that inhabit the host's intestine influence many aspects of the host's health and bear the adaptive potential to alterations in harsh environments and diets. The Qinghai-Tibet Plateau represents one of the harshest environments in the world. Preliminary progress has been made in identifying the communities of gut microbes in Indigenous Tibetans and non-human animals. However, due to the complexity of microbial communities, the effects of gut microbes on the host's health and high-plateau adaptation remain unexplained. Herein, we review the latest progress in identifying factors affecting the gut microbiota of native Tibetans and non-human animals and highlight the complex interactions between the gut microbiota, health and highland adaptation, which provides a basis for exploring the correlations between the gut microbiota and clinical indexes in native highland residents and travellers, as well as developing microbiota-based strategies to mitigate health risks for tourists and treatments for mountain sickness during high-altitude travel in the future.

Temporal and nutritional effects on the weaner pig ileal microbiota

BACKGROUND

The porcine gastrointestinal microbiota has been linked to both host health and performance. Most pig gut microbiota studies target faecal material, which is not representative of microbiota dynamics in other discrete gut sections. The weaning transition period in pigs is a key development stage, with gastrointestinal problems being prominent after often sudden introduction to a solid diet. A better understanding of both temporal and nutritional effects on the small intestinal microbiota is required. Here, the development of the porcine ileal microbiota under differing levels of dietary protein was observed over the immediate post-weaning period.

RESULTS

Ileal digesta samples were obtained at post-mortem prior to weaning day (day - 1) for baseline measurements. The remaining pigs were introduced to either an 18% (low) or 23% (high) protein diet on weaning day (day 0) and further ileal digesta sampling was carried out at days 5, 9 and 13 post-weaning. We identified significant changes in microbiome structure (P = 0.01), a reduction in microbiome richness (P = 0.02) and changes in the abundance of specific bacterial taxa from baseline until 13 days post-weaning. The ileal microbiota became less stable after the introduction to a solid diet at weaning (P = 0.036), was highly variable between pigs and no relationship was observed between average daily weight gain and microbiota composition. The ileal microbiota was less stable in pigs fed the high protein diet (P = 0.05), with several pathogenic bacterial genera being significantly higher in abundance in this group. Samples from the low protein and high protein groups did not cluster separately by their CAZyme (carbohydrate-active enzyme) composition, but GH33 exosialidases were found to be significantly more abundant in the HP group (P = 0.006).

CONCLUSIONS

The weaner pig ileal microbiota changed rapidly and was initially destabilised by the sudden introduction to feed. Nutritional composition influenced ileal microbiota development, with the high protein diet being associated with an increased abundance of significant porcine pathogens and the upregulation of GH33 exosialidases-which can influence host-microbe interactions and pathogenicity. These findings contribute to our understanding of a lesser studied gut compartment that is not only a key site of digestion, but also a target for the development of nutritional interventions to improve gut health and host growth performance during the critical weaning transition period.

Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency

The composition of the gut microbiome plays important roles in digestion, nutrient absorption, and health. Here, we analyzed the microbial composition in the duodenum and ileum of yellow broilers. Chickens were grouped based on feed efficiency (high feed efficiency [HFE] and low feed efficiency [LFE] groups; n = 22 each). Microbial samples from the duodenum and ileum were collected, and 16S rRNA sequencing of the V3–V4 region was performed. The dominant bacteria in the duodenum were from the phyla Firmicutes and Cyanobacteria and the genera Lactobacillus, Faecalibacterium, and Ruminococcus. In the ileum, the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, SMB53 and Enterococcus were predominant. Alpha diversity analysis showed that the microbiota diversity was significantly higher in the duodenum than in the ileum. The structure of the ileal microbiota was similar between groups, and the species richness of the microbiota in the HFE group was significantly higher than that in the LFE group. In the HFE and LFE groups, Firmicutes and Cyanobacteria were negatively correlated, and Lactobacillus had medium to high negative correlations with most other genera. Functional prediction analysis showed that the gluconeogenesis I pathway was the most abundant differential metabolic pathway and was significantly altered in the LFE group. Moreover, although the microbial community structures were similar in the duodenum and ileum, the diversity of the microbial community was significantly higher in the duodenum than in the ileum. Pearson correlation analysis revealed that the phylum Chloroflexi and genera Acinetobacter, Pseudomonas, Bacillus and Neisseria were with coefficients <−0.3 or >0.3. In the ileum, Ruminococcus may be associated with HFE whereas Faecalibacterium may be associated with LFE. These findings may provide valuable foundations for future research on composition and diversity of intestinal microbes and provide insights into the roles of intestinal microbes in improving feed efficiency and the industrial economic benefits of yellow broilers.

Effect of Synbiotics on Amelioration of Intestinal Inflammation Under Hypobaric Hypoxia

Khanna, Kunjan, Kamla Prasad Mishra, Sudipta Chanda, Lilly Ganju, Shashi Bala Singh, and Bhuvnesh Kumar. Effect of synbiotics on amelioration of intestinal inflammation under hypobaric hypoxia. High Alt Med Biol. 22:32-44, 2021. Aim: High-altitude exposure alters the gastrointestinal (GI) system, which may be a cause of hypobaric hypoxia (HH)-induced microbial dysbiosis. Therefore, we investigated the effect of a combination of beneficial bacteria and nondigestible fiber popularly known as "synbiotics" (Syn) to mitigate intestinal inflammation and microbial dysbiosis post-HH exposure. Methods: Syn, that is, a combination of probiotics and prebiotics, was given to male Sprague-Dawley rats 3 days prior and along with the HH exposure to assess its effect on mucosal barrier injury and inflammation. Changes in the gut microbiota and functional analysis were assessed using 16S rRNA and whole-genome sequencing (WGS) analysis. Results: Syn treatment significantly improved mucosal barrier injury in terms of decreased serum fluorescein isothiocyanate dextran from 96.1 ± 7.95 μg/ml in HH-alone group to 38.35 ± 4.55 μg/ml in HH + Syn group (p < 0.01) and decreased serum zonulin levels, that is, from 134.7 ± 19.05 ng/ml (HH alone) to 64.02 ± 7.33 ng/ml (HH + Syn) (p < 0.05), along with improvement in the intestinal villi under HH exposure. Levels of proinflammatory cytokines and chemokines significantly reduced upon Syn treatment, indicating attenuation of inflammation and immune cell migration. Syn treatment significantly reduced Th17 biased immune response preventing interleukin (IL)-17-induced inflammatory response with 8.1 ± 0.5 ng/mg protein in HH exposure group, while treatment with Syn in HH-exposed group reduced IL-17 levels to 2.01 ± 0.3 ng/mg protein (p < 0.001). Analysis of 16S rRNA showed significant (p < 0.05) alterations in Deferribacteres, Firmicutes, and Verrucomicrobia at the phylum levels, whereas Prevotella, Paenibacillus, Clostridium, Turicibacter, Bacillus, Anoxybacillus, Enterococcus, SMB53, Mucispirillum, Allobaculum, and Lactococcus were significantly altered (p < 0.05) in abundance at the genus level. WGS analysis revealed improvement in GI health by regulating functional pathways post-Syn treatment. Conclusion: Our findings indicate that Syn treatment improves intestinal barrier function and curtailed inflammation in the HH-exposed rat models, proving it to be a promising potential countermeasure for HH-induced gut problems.

Combined process of bio-contact oxidation-constructed wetland for blackwater treatment

In this study, a combined process of bio-contact oxidation and constructed wetland for blackwater treatment was assessed. The effects of hydraulic retention time and particle size on treatment performance were systematically studied. Additionally, microbial communities in the combined process were characterized. The results show that the removal efficiency of COD, TN, NH₄⁺-N, and TP under optimum conditions in this study were 81.6%, 56.1%, 42.2%, and 73.7%, respectively. The maximum nitrogen removal rate reached 16.5 g m^-2 d^-1 (3 d). N and P removed via direct plant absorption accounted for only 19.7% and 16.1% of the total system, respectively. Plants play a crucial role in the microbial community of constructed wetlands and influence the overall performance of the system. The biofilm on roots favored aerobic and heterotrophic bacteria such as the aerobic denitrification microorganisms of Pelagibacterium, Halomonas, and Zoogloea. Overall, the combined process is a suitable technique for the treatment of blackwater.

The Bacterial Microbiome in the Small Intestine of Hooded Seals (Cystophora cristata)

Arctic hooded seals (Cystophora cristata) are monogastric carnivores that go through extreme fasting and re-feeding in early life. They are born isolated on sea ice; suckle high-fat milk for four days and may then fast for up to one month before they start hunting and feeding on small prey (fish and crustaceans). Previous studies of the gut microbiota in pinnipeds have focused on the large intestine, while little data exist on the small intestinal microbiota. In this study, the bacterial microbiome in the proximal and distal small intestine of four captive two-year old seals (two males and two females) fed herring (Clupea harengus) was sampled post-mortem and characterized using 16S rRNA metabarcoding from the V1–V3 hypervariable region of the 16S ribosomal RNA (rRNA) genes. The seals were originally born in the wild and taken into human care at the end of the suckling period. Molecular-based analysis using Illumina Hiseq resulted in 569,910 16S rRNA sequences from the four seals (both sampling sites together). Taxonomical classification applying a naive Bayesian algorithm gave 412 Operational Taxonomic Units (OTUs). Firmicutes was the major phylum across samples (Proximal (P): 90.5% of total sequences, on average; Distal (D): 94.5%), followed by Actinobacteria (P: 7%; D: 0.3%) and Proteobacteria (P: 1.7%; D: 1.9%). Bacterial spp. belonging to the Clostridium (P: 54.1%; D: 41.6%) and SMB53 (P: 15.3%; D: 21.5%) constituted the major genera in both the proximal and distal small intestine. Furthermore, comparison with hindgut and fecal samples from geographically diverse marine mammals highlighted similarities in the microbiome between our seals and those sharing similar aquatic environments. This study has provided a first reliable glimpse of the bacterial microbiota in the small intestine microbiome of hooded seals.

Characterisation and comparison of the mucosa-associated bacterial communities across the gastrointestinal tract of stranded green turtles, Chelonia mydas

Chelonia mydas are primarily herbivorous long-distance migratory sea turtles that contribute to marine ecosystems. Extensive research has been conducted to restore the populations of green turtles. Little is known about their gut microbiota which plays a vital role in their health. We investigated the mucosa-associated bacterial communities across the gastrointestinal (GI) tract of a total four (3, juvenile and 1, adult) stranded green turtles. Samples taken from four GI regions including oesophagus, stomach, small intestine and large intestine were analysed by high-throughput sequencing targeting hypervariable V1-V3 regions of the bacterial 16S rRNA gene. Bacterial diversity and richness decreased longitudinally along the GI tract from oesophagus to the small intestine of stranded turtles. The large intestine showed a higher bacterial diversity and richness compared to small intestine. The bacterial community of green turtles' GI tract was largely dominated by Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Aerobic and facultative anaerobic bacteria prevailed primarily in the oesophagus while anaerobes (Lachnospiraceae, Peptostreptococcaceae and Ruminococcaceae) constituted the bulk of large intestinal microbiota. Firmicutes dominated the GI tract except within the small intestine where Proteobacteria prevailed. At the OTU level, six percent of the total OTUs (>1% relative abundance) were common in all GI regions. This is a comprehensive characterisation of bacterial microbiota across the GI tract in green turtles which will provide a reference for future studies on turtle gut microbiome and their metabolism to improve their health and nutrition during rehabilitation.

Interspecific comparison of the fecal microbiota structure in three Arctic migratory bird species

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink-footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink-footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink-footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink-footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink-footed geese was discussed to be related with their herbivorous diet.

Captivity Influences Gut Microbiota in Crocodile Lizards (Shinisaurus crocodilurus)

Captivity is an important measure for conservation of an endangered species, and it is becoming a hot topic in conservation biology, which integrates gut microbiota and endangered species management in captivity. As an ancient reptile, the crocodile lizard (Shinisaurus crocodilurus) is facing extreme danger of extinction, resulting in great significance to species conservation in the reserve. Thus, it is critical to understand the differences in gut microbiota composition between captive and wild populations, as it could provide fundamental information for conservative management of crocodile lizards. Here, fecal samples of crocodile lizards were collected from two wild and one captive populations with different ages (i.e., juveniles and adults) and were analyzed for microbiota composition by 16S ribosomal RNA (rRNA) gene amplicon sequencing. This study showed that the lizard gut microbiota was mainly composed of Firmicutes and Proteobacteria. The gut microbiota composition of crocodile lizard did not differ between juveniles and adults, as well as between two wild populations. Interestingly, captivity increased community richness and influenced community structures of gut microbiota in crocodile lizards, compared with wild congeners. This was indicated by higher abundances of the genera Epulopiscium and Glutamicibacter. These increases might be induced by complex integration of simple food resources or human contact in captivity. The gut microbiota functions of crocodile lizards are primarily enriched in metabolism, environmental information processing, genetic information processing, and cellular processes based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This study provides fundamental information about the gut microbiota of crocodile lizards in wild and captive populations. In the future, exploring the relationship among diet, gut microbiota, and host health is necessary for providing animal conservation strategies.

Microbiome diversity and composition varies across body areas in a freshwater turtle

There is increasing recognition that microbiomes are important for host health and ecology, and understanding host microbiomes is important for planning appropriate conservation strategies. However, microbiome data are lacking for many taxa, including turtles. To further our understanding of the interactions between aquatic microbiomes and their hosts, we used next generation sequencing technology to examine the microbiomes of the Krefft's river turtle (Emydura macquarii krefftii). We examined the microbiomes of the buccal (oral) cavity, skin on the head, parts of the shell with macroalgae and parts of the shell without macroalgae. Bacteria in the phyla Proteobacteria and Bacteroidetes were the most common in most samples (particularly buccal samples), but Cyanobacteria, Deinococcus-thermus and Chloroflexi were also common (particularly in external microbiomes). We found significant differences in community composition among each body area, as well as significant differences among individuals. The buccal cavity had lower bacterial richness and evenness than any of the external microbiomes, and it had many amplicon sequence variants (ASVs) with a low relative abundance compared to other body areas. Nevertheless, the buccal cavity also had the most unique ASVs. Parts of the shell with and without algae also had different microbiomes, with particularly obvious differences in the relative abundances of the families Methylomonaceae, Saprospiraceae and Nostocaceae. This study provides novel, baseline information about the external microbiomes of turtles and is a first step in understanding their ecological roles.

Characterization of the microbiome along the gastrointestinal tracts of semi-artificially reared bar-headed geese (Anser indicus)

As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.

Dietary Recombinant Phycoerythrin Modulates the Gut Microbiota of H22 Tumor-Bearing Mice

Normal intestinal flora is widely involved in many functions of the host: nutritional metabolism; maintenance of intestinal microecological balance; regulation of intestinal endocrine function and nerve signal transduction; promotion of intestinal immune system development and maturation; inhibition of pathogenic bacteria growth and colonization, reduction of its invasion to intestinal mucosa, and so on. In recent years, more and more studies have shown that intestinal flora is closely related to the occurrence, development, and treatment of various tumors. It is indicated that recombinant phycoerythrin (RPE) has significant anti-tumor and immunomodulatory effects. However, little is known about the mechanism of the effect of oral (or intragastric) administration of RPE on gut microbiota in tumor-bearing animals. In this study, using high-throughput 16S rDNA sequencing, we examined the response of gut microbiota in H22-bearing mice to dietary RPE supplementation. The results showed that the abundance of beneficial bacteria in the mice intestinal flora decreased and that of the detrimental flora increased after inoculation with tumor cells (H22); following treatment with dietary RPE, the abundance of beneficial bacteria in the intestinal flora significantly increased and that of detrimental bacteria decreased. In this study, for the first time, it was demonstrated that dietary RPE could modulate the gut microbiota of the H22 bearing mice by increasing the abundance of beneficial bacteria and decreasing that of detrimental bacteria among intestinal bacteria, providing evidence for the mechanism by which bioactive proteins affect intestinal nutrition and disease resistance in animals.

Bacterial diversity in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster in Henan Province, China

Purpose

Previous studies have assessed the diversity of gastrointestinal bacteria in bats and reported that some of the strains are pathogenic to humans; therefore, bats are considered to be potential reservoirs of zoonotic pathogens. However, the bacterial diversity and types of pathogenic bacteria in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster have not yet been determined. Humans frequently come into contact with these species; therefore, assessments of their gut microbiota, especially potential pathogens, are essential for public health. In the present study, MiSeq high-throughput sequencing was used to address this research gap, and the results were compared with those reported previously.

Methods

The V3–V4 regions of the 16S rRNA gene were sequenced using the MiSeq high-throughput sequencing platform to determine the bacterial community of the stomach and the intestines of R. luctus and M. leucogaster.

Results

The bacteria in the gastrointestinal tracts of R. luctus and M. leucogaster were classified into three and four main bacterial phyla, respectively. In both R. luctus and M. leucogaster, the dominant phylum was Proteobacteria (stomach 86.07% and 95.79%, intestines 91.87% and 88.78%, respectively), followed by Firmicutes (stomach 13.84% and 4.19%, intestines 8.11% and 11.20%, respectively). In total, 18 and 20 bacterial genera occurred in a relative abundance of 0.01% or more in the gastrointestinal tracts of R. luctus and M. leucogaster, respectively. In R. luctus, the dominant genera were Lactococcus (10.11%) and Paeniclostridium (3.41%) in the stomach, and Undibacterium (28.56%) and Paeniclostridium (4.69%) in the intestines. In M. leucogaster, the dominant genera were Undibacterium (54.41%) and Burkholderia (5.28%) in the stomach, and Undibacterium (29.67%) and Enterococcus (7.19%) in the intestines. Among the detected gastrointestinal tract flora of R. luctus and M. leucogaster, 12 bacterial genera were pathogenic or opportunistic pathogens.

Conclusion

A high number of human pathogens were detected in the gastrointestinal tracts of R. luctus and M. leucogaster, which demonstrates the urgency for increased efforts in the prevention and management of bat-to-human disease transmission from these species.

Baby-SPIME: A dynamic in vitro piglet model mimicking gut microbiota during the weaning process

The study aimed to adapt the SHIME® model, developed to simulate human digestion and fermentation, to a baby-SPIME (baby Simulator of Pig Intestinal Microbial Ecosystem). What constitutes a unique feature of this model is its twofold objective of introducing an ileal microbial community and mimicking a dietary weaning transition. This model should then be ideally suited to test the dietary weaning strategies of piglets in vitro. Regarding the microbiota, the main phyla making up the model were Firmicutes, Bacteroidetes and Proteobacteria although Bacteroidetes decreased after inoculation (p = 0.043 in ileum, p = 0.021 in colon) and Delta-Proteobacteria were favoured (p = 0.083 in ileum, p = 0.043 in colon) compared to Gamma-Proteobacteria. The designed model led to a low representation of Bacilli - especially Lactobacillus sp. in the ileum and a weak representation of Bacteroidia in the proximal colon. However, Mitsuokella and Prevotella were part of the major genera of the model along with Bifidobacterium, Fusobacterium, Megasphaera and Bacteroides. As a result of weaning, two major changes - normally occurring in vivo - were detected in the system: firstly, Firmicutes diminished when Bacteroidetes increased particularly in the proximal colon; secondly, Bacteroides decreased and Prevotella increased (mean value for four runs). In terms of metabolite production, while a ratio acetate: propionate: butyrate of 60:26:14 was obtained in post-weaned colon, the expected inversion of the ratio propionate: butyrate in the post-weaned ileum was unfortunately not observed. To conclude, the so-called baby-SPIME model meets expectations regarding the resident microbiota of the proximal colon bioreactor and the metabolites produced thereof. In terms of the evolution of major groups of bacteria, the in vitro weaning process appeared to be successful. However, higher concentration of butyric acid would have been expected in ileum part of newly weaned piglets, as observed in vivo. The microbiota in the ileum bioreactor seemed in fact to act like a pre-colon. This suggests that microbial profile in ileum bioreactor had to be improved.

Combined propidium monoazide pretreatment with high-throughput sequencing evaluated the bacterial diversity in chicken skin after thermal treatment

AIMS

The purpose of this experiment was to study the bacterial diversity and predominance of spoilage bacteria in chicken skin at different thermal treatment temperatures (60, 70, 80, 90, 100, 110, 120°C).

METHOD AND RESULTS

Bacteria in chicken skin was collected, then propidium monoazide treatment to remove the DNA of dead cell, total DNA was extracted by Tiandz Bacterial DNA Kit, and investigated by high-throughput sequencing of the v3/v4 regions of the 16S rDNA gene. A total of 796 008 high-quality bacterial sequences were obtained for assessing the microbial diversity of chicken skin from seven thermal treatment group and control group. The results showed that the bacterial diversity in chicken skin at 90°C was lowest. And Acinetobacter (25·88%), Clostridium (20·70%), Bacteroides (13·93%) and Myroides (13·13%) were the main flora at 25°C; The Clostridium was dominant genus of the samples heat-treated by 60, 70, 80 and 90°C, the proportion of this genus were up to 64·86, 77·42, 52·22 and 87·30% respectively. The Bacillus was the main flora of the samples heat-treated by 100, 110 and 120°C, and the relative percentages were 39·44, 79·61 and 45·96% respectively. In addition, high-temperature-resistant Serratia was found in chicken skin.

CONCLUSIONS

The study revealed that the relationship between thermal treatment temperature and bacterial diversity and dominant spoilage bacteria in chicken skin, which had a strong guiding significance for the control and prediction of micro-organisms in foods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this paper could provide a theoretical basis for meat products containing chicken skin, including the safe use of chicken skin, determination of sterilization process parameters and selection of preservatives for compounding, which has strong practicality in China.

Comparative Analysis of Intestine Microbiota of Four Wild Waterbird Species

Waterbirds are ubiquitous and globally distributed. Yet, studies on wild waterbirds' gut microbiota are still rare. Our aim was to explore and compare the gut microbial community composition of wild waterbird species. Four wild waterbird species that are either wintering or all-year residents in Israel were studied: great cormorants, little egrets, black-crowned night herons and black-headed gulls. For each bird, three intestinal sections were sampled; anterior, middle and posterior. No significant differences were found among the microbiota compositions in the three intestine sections of each individual bird. Each waterbird species had a unique microbial composition. The gut microbiota of the black-headed gulls' fundamentally deviated from that of the other bird species, probably due to a very high abundance (58.8%) of the genus Catellicoccus (Firmicutes). Our results suggest a correlation between the waterbird species' phylogeny and their intestine microbial community hierarchical tree, which evinced phylosymbiosis. This recent coinage stands for eco-evolutionary patterns between the host phylogeny and its microbiota composition. We conclude that eco-evolutionary processes termed phylosymbiosis may occur between wild waterbird species and their gut microbial community composition.

Hindgut Bacterial Flora Analysis in Oriental Honey Buzzard (Pernis ptilorhynchus)

The intestinal microbiome is known to affect host health through various effects on nutrition and immunity. The oriental honey buzzard (OHB) is a raptor that feeds on bees and wasps. Due to its restricted diet, we reasoned that the OHB may have a unique microbiome. The aim of this study was to characterize the structure of the intestinal flora of oriental honey buzzards and to investigate the difference of intestinal bacterial flora between individuals in the wild and those reared in captivity. We investigated the intestinal microbiome of seven wild buzzards (Wild), one zoo-reared (Zoo), and one individual reared in captivity for one month (Rearing). Average operational taxonomic units in Wild and Rearing were 69.4 and 113, respectively. Diversity indices such as ACE, Chao 1, Shannon, and Alpha were significantly lower in the Wild than in the Rearing samples. These results suggest that the variety of Wild microbiome is remarkably low. At the phylum level, the composition of the microbiome was similar in all three groups, with firmicutes and bacteroidetes predominating. The third most abundant bacterium in Wild was Proteobacteria, whereas it was Actinobacteria in Rearing and unclassified bacteria in Zoo. Thus, microbiome composition is affected even with just one month of human rearing.

Gut microbiota correlates with fiber and apparent nutrients digestion in goose

To explore the relationship among the level of fiber, gut microbiota, and nutritional substances, we applied the next generation sequencing technology for the identification of the composition and structure of microbiota in the gastrointestinal tract. In this study, a total of 25 phyla and 298 genera were identified from the gastrointestinal tract; Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla. The ability of cecum in carbohydrate metabolism was significantly higher than that of the gizzard and ileum (P < 0.05). The bacterial community structure in various stages of the development of the cecum was different. In the different growth stages of cecum, the increase in the microbiota structure of the fiber level elevates the ability of carbon hydration. Second, the apparent metabolic rates of the other nutrients were affected by the fiber and period except for acid detergent fiber (P < 0.05); the apparent utilization rate of the nutrients increased with time. However, with the increase in the fiber level, the apparent utilization of nutrients was initially increased, followed by a decrease. Therefore, a correlation was established between the fiber level and gastrointestinal microbiota and apparent nutrient utilization rate of the 3 phyla. Our results suggest that the fiber level and growth stages could impact the composition of gut microbiota.

Black water collected from the septic tank treated with a living machine system: HRT effect and microbial community structure

In this study, the performance of a living machine (LM) system was evaluated for use in the treatment of black water collected from septic tanks with hydraulic retention times (HRTs) of 6, 5, and 4 days. We found that the HRT had little effect on the removal efficiency of chemical oxygen demand (COD). However, the removal rates of total nitrogen (TN) and ammonium nitrogen (NH₄⁺-N) decreased with the reduction of HRT, whereas the removal efficiency of total phosphate (TP) was consistently low because of the long sludge retention time. The working conditions of #1 achieved the highest removal efficiency of COD (85%), NH₄⁺-N (75%), and TN (47%), although the removal efficiency of TP (11%) was slightly lower than that of #2 (12%). The microbial communities in each tank of the LM system were characterized by high-throughput sequencing, which showed that the LM system successfully created more favorable conditions for fermentative bacteria than traditional systems, with relative abundances of 13% (#1), 13% (#2), and 15% (#3) compared to that of the anaerobic/anoxic/oxic (A²O) system (<3%). Smithella was the dominant fermentative bacteria, accounting for 9% (#1), 7% (#2), and 10% (#3) of total bacteria in the LM system. The relative abundances of ammonia oxidizing bacteria (AOB) (12%) and anaerobic ammonium oxidizing bacteria (AnAOB) (7%) in the LM system were much higher than that in the A²O system. Overall, the LM system offered a more sustainable and economical solution for treating black water.

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese

Gut microbial ecology is responsible for fatty acid metabolism in ruminants. The cecal microbiota composition of geese and their adaptation to fiber inclusion and feeding timeswere investigated in this study. A total of 116 Wanxi white geese were randomly selected at 70 days old. Eight geese were subjected to cecal sampling at 70 d of age, and the remaining 108 geese were divided into four groups with three replicates each (9 geese in each replicate). The geese in the four groups were fed 0, 15, 30, and 45% green forage (relative to dry matter), respectively. Three birds from each replicate were selected for cecal sampling at 80, 90, and 100 days old. All samples were subjected to 16S rRNA gene sequencing using the Illumina Ion Personal Genome Machine platform. Bacterial abundance was analyzed using two-way ANOVA analysis, and the relationship between the relative abundance of bacteria (phylum level) and fatty acids was analyzed using acanonical correspondence analysis. Cecal microbiota in geese were mainly composed of Bacteroidetes (68.46%), Firmicutes (20.04%), and Proteobacteria (7.89%). Dietary treatments had no significant effect on the α-diversity indices of the cecal bacterial community (P > 0.05), but a numerical increase occurred with increased fattening duration and green forage inclusion. The Selenomonadales order (P = 0.024), Negativicutes class (P = 0.026), and Megamonas (P = 0.012) and Oscillospira (P = 0.042) genera were affected by green forageinclusion level, and microflora abundance was mainly influenced by the fattening duration. Bacteria phyla were mostly set along the line of linolenic acid and oleic acid. Finally, Bacteroidales might be an intestinal promoter that improves unsaturated fatty acid synthesis in geese.

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes, Proteobacteria, and Fusobacteria, in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate‐active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds.

Effects of mixed lactic acid bacteria on intestinal microbiota of mice infected with Staphylococcus aureus

Background

The stability of intestinal microorganisms plays an important role in human health, as the intestines perform important functions in the human body. Staphylococcus aureus is a Gram-positive, facultative anaerobic bacteria, it causes human infection worldwide, and is a major pathogen that causes intestinal infection. Mixed lactic acid bacteria (LAB) may have potential in the prevention and treatment of S. aureus infection. In the present study, we examined the effects of mixed LAB treatment on intestinal microbiota modulation in mice infected with S. aureus.

Results

High-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene showed that the mixed LAB maintained the richness and diversity of the microbiota in the mouse intestine. By establishing operational taxonomic units and using rarefaction analysis, rank-abundance distribution curves, heat maps, Venn diagrams, bacterial community structures, and hierarchical clustering analysis, Bacteroidales, Lachnospiraceae, Bacteroides and Prevotellaceae were the most abundant taxa in the samples, we found that the composition of the intestinal microbiota was similar between the protection group administered mixed LAB and the negative control group.

Conclusions

Staphylococcus aureus destroys the stable intestinal microbiota structure of mice, treatment with mixed LAB could prevent S. aureus infection in mice and improve the structure of the intestinal microbiota.

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds

The digestive tract microbiota (DTM) plays a plethora of functions that enable hosts to exploit novel niches. However, our understanding of the DTM of birds, particularly passerines, and the turnover of microbial communities along the digestive tract are limited. To better understand how passerine DTMs are assembled, and how the composition changes along the digestive tract, we investigated the DTM of seven different compartments along the digestive tract of nine New Guinean passerine bird species using Illumina MiSeq sequencing of the V4 region of the 16S rRNA. Overall, passerine DTMs were dominated by the phyla Firmicutes and Proteobacteria. We found bird species-specific DTM assemblages and the DTM of different compartments from the same species tended to cluster together. We also found a notable relationship between gut community similarity and feeding guilds (insectivores vs. omnivores). The dominant bacterial genera tended to differ between insectivores and omnivores, with insectivores mainly having lactic acid bacteria that may contribute to the breakdown of carbohydrates. Omnivorous DTMs were more diverse than insectivores and dominated by the bacterial phyla Proteobacteria and Tenericutes. These bacteria may contribute to nitrogen metabolism, and the diverse omnivorous DTMs may allow for more flexibility with varying food availability as these species have wider feeding niches. In well-sampled omnivorous species, the dominant bacterial genera changed along the digestive tracts, which was less prominent for insectivores. In conclusion, the DTMs of New Guinean passerines seem to be species specific and, at least in part, be shaped by bird diet. The sampling of DTM along the digestive tract improved capturing of a more complete set of members, with implications for our understanding of the interactions between symbiont and gut compartment functions.

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef

Green turtles (Chelonia mydas) are endangered marine herbivores that break down food particles, primarily sea grasses, through microbial fermentation. However, the microbial community and its role in health and disease is still largely unexplored. In this study, we investigated and compared the fecal bacterial communities of eight wild-captured green turtles to four stranded turtles in the central Great Barrier Reef regions that include Bowen and Townsville. We used high-throughput sequencing analysis targeting the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. At the phylum level, Firmicutes predominated among wild-captured green turtles, followed by Bacteroidetes and Proteobacteria. In contrast, Proteobacteria (Gammaproteobacteria) was the most significantly dominant phylum among all stranded turtles, followed by Bacteroidetes and Firmicutes. In addition, Fusobacteria was also significantly abundant in stranded turtles. No significant differences were found between the wild-captured turtles in Bowen and Townsville. At the family level, the core bacterial community consisted of 25 families that were identified in both the wild-captured and stranded green turtles, while two unique sets of 14 families each were only found in stranded or wild-captured turtles. The predominance of Bacteroides in all groups indicates the importance of these bacteria in turtle gut health. In terms of bacterial diversity and richness, wild-captured green turtles showed a higher bacterial diversity and richness compared with stranded turtles. The marked differences in the bacterial communities between wild-captured and stranded turtles suggest the possible dysbiosis in stranded turtles in addition to potential causal agents.

Comparison of gizzard and intestinal microbiota of wild neotropical birds

Gut bacterial communities have been shown to be influenced by diet, host phylogeny and anatomy, but most of these studies have been done in captive animals. Here we compare the bacterial communities in the digestive tract of wild birds. We characterized the gizzard and intestinal microbiota among 8 wild Neotropical bird species, granivorous or frugivorous species of the orders Columbiformes and Passeriformes. We sequenced the V4 region of the 16S rRNA gene in 94 collected samples from 32 wild birds from 5 localities, and compared bacterial communities by foraging guild, organ, locality and bird taxonomy. 16S rRNA gene-based sequencing data were examined using QIIME with linear discriminant analysis effect size (LEfSe) and metabolic pathways were predicted using PICRUSt algorism. We identified 8 bacterial phyla, dominated by Firmicutes, Actinobacteria and Proteobacteria. Beta diversity analyses indicated significant separation of gut communities by bird orders (Columbiformes vs. Passerifomes) and between bird species (p<0.01). In lower intestine, PICRUSt shows a predominance of carbohydrate metabolism in granivorous birds and xenobiotics biodegradation pathways in frugivorous birds. Gizzard microbiota was significantly richer in granivorous, in relation to frugivorous birds (Chao 1; non-parametric t-test, p<0.05), suggesting a microbial gizzard function, beyond grinding food. The results suggest that the most important factor separating the bacterial community structure was bird taxonomy, followed by foraging guild. However, variation between localities is also likely to be important, but this could not been assessed with our study design.

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition

Nutrition and health of northern white-cheeked gibbons (Nomascus leucogenys) are considered to be primarily influenced by the diversity of their gastrointestinal tract (GIT) microbiota. However, the precise composition, structure, and role of the gibbon GIT microbiota remain unclear. Microbial communities from the GITs of gibbons from Nanning (NN, n = 36) and Beijing (BJ, n = 20) Zoos were examined through 16S rRNA sequencing. Gibbon’s GITs microbiomes contained bacteria from 30 phyla, dominated by human-associated microbial signatures: Firmicutes, Bacteroidetes, and Proteobacteria. Microbial species richness was markedly different between adult gibbons (>8 years) under distinct captive conditions. The relative abundance of 14 phyla varied significantly in samples of adults in BJ versus NN. Among the age groups examined in NN, microbiota of adult gibbons had greater species variation and richer community diversity than microbiota of nursing young (<6 months) and juveniles (2–5 years). Age-dependent increases in the relative abundances of Firmicutes and Fibrobacteres were detected, along with simultaneous increases in dietary fiber intake. A few differences were detected between sex cohorts in NN, suggesting a very weak correlation between sex and GIT microbiota. This study is the first to taxonomically identify gibbon’s GITs microbiota confirming that microbiota composition varies with age and captive condition.

Blackwater treatment using vertical greening: Efficiency and microbial community structure

This study assesses the use of vertical greening for blackwater treatment. The effects of hydraulic retention time (HRT) and drip frequency on treatment performance were systematically studied. Additionally, microbial communities in the vertical greening system were characterized. The results show that the removal efficiencies of NH₄⁺-N and total phosphate (TP) increased with an increase in HRT, and the drip frequency had a significant effect on TP. High-throughput sequencing revealed that the diversity of the microbial community did not change significantly along vertical and horizontal directions, but the dominant species shifted. Heterotrophic nitrifying and denitrifying bacteria decreased significantly while autotrophic nitrifying bacteria, especially ammonia oxidizing bacteria, proliferated in a vertical direction. Therefore, it is concluded that vertical greening systems can effectively treat blackwater and lower NH⁺-N levels.

Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene

Stranded green turtles (Chelonia mydas) are often cared for in rehabilitation centers until they recover. Although the specific causal agents of diseases in stranded turtles are difficult to diagnose, we know that gut microbiota of green turtles play a vital role in health as well as a wide range of diseases. The objective of this study was to characterize and compare the gut bacterial communities between pre-hospitalization (PH) and post-rehabilitation (PR) stranded green turtles using high-throughput sequencing analysis targeting V1-V3 regions of the bacterial 16S rRNA gene. A total of eight cloacal swab samples were collected from four green turtles undergoing rehabilitation. Proteobacteria dominating in both PH and PR samples without any significant difference. Firmicutes was the second and Bacteroidetes was the third most abundant phylum in PH samples, while Bacteroidetes prevailed in PR samples, followed by Firmicutes. The predominance of the genus Bacteroides in both PH and PR samples indicates the importance of this genus in turtle gut health. At a class level, Epsilonproteobacteria was significantly (P<0.05) associated with PH samples and Deltaproteobacteria predominated (P<0.05) in PR samples. The significant abundance of Campylobacter fetus, Escherichia coli, Clostridium botulinum and Vibrio parahaemolyticus in PH samples indicate pathogenic associations with stranded green turtles with zoonotic potential. The presence of Salmonella enterica in only PR samples suggest possible acquisition of this bacteria during rehabilitation. In this study, all post-rehabilitation green turtles exhibited similar bacterial communities, irrespective of their microbial compositions at pre-hospitalization. The marked differences in the gut bacterial communities of PH and PR turtles indicate the outcome of dietary, management and environmental shift during rehabilitation. Therefore, it is important to address the process of restoring normal gut microbiota of recovered turtles prior to release back to their natural habitat.

Great cormorants (Phalacrocorax carbo) as potential vectors for the dispersal of Vibrio cholerae

Vibrio cholerae is the cause of cholera, a devastating epidemic and pandemic disease. Despite its importance, the way of its global dissemination is unknown. V. cholerae is abundant in aquatic habitats and is known to be borne by copepods, chironomids and fishes. Our aim was to determine if fish-eating birds act as vectors in the spread of V. cholerae by consuming infected fish. We determined the existence of V. cholerae in the microbiome of 5/7 wild cormorants’ intestine. In three of these V. cholerae-positive wild cormorants, the presence of a gene for cholera toxin (ctxA) was detected. We subsequently tested eight captive, hand-reared cormorants, divided into two equal groups. Prior to the experiment, the feces of the cormorants were V. cholerae-negative. One group was fed exclusively on tilapias, which are naturally infected with V. cholerae, and the other was fed exclusively on goldfish or on koi that were V. cholerae-negative. We detected V. cholerae in the feces of the tilapia-fed, but not in the goldfish/koi-fed, cormorants. Hence, we demonstrate that fish-eating birds can be infected with V. cholerae from their fish prey. The large-scale movements of many fish-eating birds provide a potential mechanism for the global distribution of V. cholerae.

Mixed Lactobacillus plantarum Strains Inhibit Staphylococcus aureus Induced Inflammation and Ameliorate Intestinal Microflora in Mice

Objective. Staphylococcus aureus is an important pathogen that causes intestinal infection. We examined the immunomodulatory function of single and mixed Lactobacillus plantarum strains, as well as their impacts on the structure of the microbiome in mice infected with Staphylococcus aureus. The experiment was divided into three groups: protection, treatment, and control. Serum IFN-γ and IL-4 levels, as well as intestinal sIgA levels, were measured during and 1 week after infection with Staphylococcus aureus with and without Lactobacillus plantarum treatment. We used 16s rRNA tagged sequencing to analyze microbiome composition. IFN-γ/IL-4 ratio decreased significantly from infection to convalescence, especially in the mixed Lactobacillus plantarum group. In the mixed Lactobacillus plantarum group the secretion of sIgA in the intestine of mice (9.4-9.7 ug/mL) was significantly higher than in the single lactic acid bacteria group. The dominant phyla in mice are Firmicutes, Bacteroidetes, and Proteobacteria. Treatment with mixed lactic acid bacteria increased the anti-inflammatory factor and the secretion of sIgA in the intestine of mice infected with Staphylococcus aureus and inhibited inflammation.