Microbiota in different digestive tract of paddlefish (Polyodon spathula) are related to their functions.

Paddlefish has high economic and ecological value. In this study, microbial diversity and community structure in intestine, stomach, and mouth of paddlefish were detected using high-throughput sequencing. The results showed that the diversity and richness indices decreased along the digestive tract, and significantly lower proportion of those were observed in intestine. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla. In top 10 phyla, there was no significant difference in mouth and stomach. But compared with intestine, there were significant differences in 8 of the 10 phyla, and Firmicutes and Bacteroidetes increased significantly, while Proteobacteria decreased significantly. There was no dominant genus in mouth and stomach, but Clostridium_sensu_stricto_1 and uncultured_bacterium_o_Bacteroidales was predominant in intestine. In conclusion, the species and abundance of microbiota in the mouth and stomach of paddlefish were mostly the same, but significantly different from those in intestine. Moreover, there was enrichment of the dominant bacteria in intestine.

Intestinal microbiota disturbance affects the occurrence of African swine fever.

Intestinal microbiota not only participates in the digestion and absorption of nutrients, but also plays an important role in regulating host metabolism and health. The current study aimed to explore the intestinal microbiota characteristics in pigs infected with African swine fever. Below the same term, fresh fecal samples of sick and healthy pigs were collected. Primers were designed and PCR was extracted based on the 16S rDNA gene of bacteria by Illumina NovaSeq sequencing platform. The results showed that the bacterial alpha diversity index of healthy pigs was significantly higher than that of sick pigs (p < 0.05). On the phylum taxa, dominant bacteria more than 98.5% in the two groups are composed of Firmicutes, Spirobacteria, and Bacteroides, of which the abundance of Firmicutes and Bacteroidetes decreased and Spiricobacteria increased extremely significant in sick pigs (p < 0.01). On the genus taxa, the relative abundance of Oscillospira, Streptococcus and Roseburia decreased significantly (p < 0.05). Most notably, Treponema performed excellently in distinguishing pigs infected with African swine fever with the abundance increased extremely significantly (p < 0.01). In conclusion, African swine fever could alter the abundance of dominant bacteria in pigs, and Treponema may be one of the important inducers for swine pathogenicity. HighlightsThe bacterial population composition in sick pigs and healthy pigs was basically similar, but the relative abundance of dominant bacteria was significantly difference.ASF could alter the abundance of dominant bacteria in pigs, and Treponema may be one of the important inducers for swine pathogenicity.These results will provide further evidence for the ASF infection in local pig farms and provide reference for their microecological control, which has important practical significance and social value for effective control of ASF, stability of pig production and guarantee of market supply.

Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

The changes of intestinal microbiota are closely related to the growth and development of animals. The current study is aimed at exploring the composition of the microbial community of pigs at different growth stages. Fresh fecal samples of three-breed hybrid pigs at three developmental stages (60, 120, and 180 days of age) were collected. The microbial composition was analyzed based on the 16S rDNA gene of bacteria Illumina NovaSeq sequencing platform. The results showed that the intestinal microbiota of pigs was distributed in 22 phyla, 46 classes, 84 orders, 147 families, and 287 genera. Firmicutes, Bacteroides, Spirochaetae, Proteobacteria, and Actinobacteria were the dominant phyla. Lactobacillus, Streptococcus, SMB53, Oscillospira, and Prevotella were the dominant genera. Among them, the abundance of Lactobacillus and SMB53 increased first and then decreased, while the change of Oscillospira was opposite. In addition, the abundance of Streptococcus increased while that of Prevotella decreased gradually. Moreover, with the increase of time and body weight, the microbial diversity showed a decreasing trend. In conclusion, the intestinal microbial composition of the three-breed hybrid pigs was relatively stable during the fattening stage, but there were significant differences in abundance.

Association of microbiota in the stomach of Sinanodonta woodiana and its cultured soil.

The current study aimed to investigate the association of microbial characteristics in the stomach of Sinanodonta woodiana (S. woodiana) and its cultured soil. S. woodiana stomach and its cultured soil were collected in winter 2019. The V3 + V4 regions of the 16S rRNA gene were sequenced to detect microbial diversity. The differences in the dominant species between S. woodiana and soil were also discussed. The results showed that the diversity and richness indices in S. woodiana were significantly higher than those in cultured soil (P < 0.01). At the phylum level, the dominant bacterial community compositions in the two groups were similar and included Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, Fusobacteria, and Acidobacteria. However, the abundance of these phyla was significantly different between the two groups (P < 0.05 or P < 0.01), and Proteobacteria was the most abundant phylum. At the genus level, a total of 1001 genera were identified in the two groups, of which 890 genera were detected in the cultured soil and 549 were detected in the S. woodiana stomach; 452 were unique to the cultured soil, and 111 were unique to the S. woodiana stomach. This result indicated great differences in the bacterial genera between the two groups. Moreover, 17 out of the 20 dominant bacterial genera exhibited statistically significant differences between the two groups (P < 0.05 or P < 0.01). Cupriavidus was the absolute dominant genus in the stomach of S. woodiana, followed by Sphingomonas and Burkholderia. The microorganisms in the stomach of S. woodiana formed a certain inherent bacterial system and were affected by the environment, which is beneficial to nutrition and health. In conclusion, the bacterial compositions were mostly the same between the stomach of S. woodiana and cultured soil, but the relative abundances of the bacterial communities were different. This study will greatly enhance the understanding of the microbial characteristics between the stomach of S. woodiana and the cultured environment, and provide guidance for healthy aquaculture in freshwater.

Intestinal microbiota characteristics of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress.

To investigate the characteristics of the intestinal microbiota of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress. Ten healthy male Kunming mice were chosen and randomly divided into control group and model group, with five mice in each group. Mice in the control group were raised regularly, while mice in the model group were treated by feeding with Folium senna decoction, restraint in a constraint tube and tail pinch with a clip for 7 days. Intestinal contents from the jejunum to ileum were collected, and DNA was extracted from each mouse. The characteristics of the intestinal microbial species were analysed by PacBio Sequel-based 16S rRNA sequencing. Result showed that alpha diversity indices in the model group were higher than those in the control group, and the Simpson index differed significantly (P < 0.05). Based on the composition and abundances of species, there were differences between the control group and model group at the species level, but these differences were not significant (P > 0.05). In the control group, Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii were the dominant species. In the model group, Staphylococcus lentus, Lactobacillus johnsonii, Candidatus arthromitus sp. SFB-mouse and Lactobacillus murinus were included. Furthermore, LEfSe analysis showed that the relative abundances of Escherichia sp. BBDP27, Helicobacter ganmani, Bacteroides vulgatus and Lactobacillus intestinalis in the model group were higher than those in the control group (P < 0.05 or P < 0.01). In conclusion, Folium senna decoction gavage combined with restraint and tail pinch stress increased the intestinal microbiota diversity. Strains associated with intestinal diseases, including Bacteroides vulgatus, Helicobacter ganmani, Staphylococcus lentus and Lactobacillus murinus, were significantly enriched, while strains beneficial to health, such as Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii, were significantly depleted.

Bacterial Diversity in the Intestinal Mucosa of Dysbiosis Diarrhea Mice Treated with Qiweibaizhu Powder.

The current research tried to explore the effect of Qiweibaizhu powder (QWBZP) on the bacterial diversity and community structure of the intestinal mucosa of dysbiosis diarrhea mice and provide a scientific basis for the efficacy of QWBZP on antibiotic-induced diarrhea. A dysbiosis diarrhea mouse model was constructed with broad-spectrum antibiotics through a mixture of cephradine capsules and gentamicin sulfate (23.33 mL·kg-1·d-1). Intestinal mucosa was collected, and DNA was extracted from each group. The bacterial characteristics in intestinal mucosa were analyzed by MiSeq sequencing based on the 16S rRNA sequencing platform. There were no significant differences in alpha diversity indices among the three groups. The sample distributions in both the normal and QWBZP groups were relatively concentrated, and the distance among individuals was close. However, an opposite result was obtained in the model group. Furthermore, the composition and abundance of species were similar between the normal group and the QWBZP group at both the phylum and genus levels. After treatment with QWBZP, the abundance of Lactobacillus increased, and Proteobacteria decreased, and the Firmicutes/Bacteroidetes ratio decreased to a normal level. Our results indicate that QWBZP can help repair mucosal bacterial structure and recover mucosal microbiota. Specifically, QWBZP increased the abundance of Lactobacillus and Bacteroidales S24-7 group norank.

Bacterial diversity in intestinal mucosa of antibiotic-associated diarrhea mice.

To probe into the mechanism of antibiotic-associated diarrhea (AAD), the bacterial diversity and composition in the intestinal mucosa of AAD mice were investigated. Twelve specific pathogen-free Kunming mice were divided into control group and model group. The mouse model of AAD was established by gavaging with antibiotics (mixture of gentamycin sulfate and cefradine) at a total dose of 23.33 ml kg-1 day-1 for 5 days continuously, twice a day. The mice in the control group were given with an equal amount of sterile water. Then, the intestinal mucosa DNA was extracted for 16S rRNA gene sequence analysis by high-throughput sequencing. The results showed that the alpha diversity of the two groups did not differ significantly from each other, while the composition of intestinal mucosa bacteria differed dramatically between the two groups. The model group showed a higher abundance of Proteobacteria and Actinobacteria. More importantly, Lactobacillus was significantly less abundant (p = 0.000), while Enterococcus was significantly more abundant (p = 0.019) in the model group than in the control group. Furthermore, antibiotic treatment increased the abundance of Citrobacter, Stenotrophomonas, and Glutamicibacter,whereas antibiotics decreased the abundance of Mycoplasma and Helicobacter. In addition, 6 and 11 unique genera were found in the control group and model group, respectively. The combination of gentamycin sulfate and cefradine changed the intestinal mucosa bacterial composition, reduced colonization resistance and damaged the intestinal mucosal barrier by reducing the abundance of Lactobacillus.

Bacterial lactase genes diversity in intestinal mucosa of dysbacterial diarrhea mice treated with Qiweibaizhu powder.

The current research tried to investigate the effect of Qiweibaizhu powder (QWBZP) on intestinal mucosa bacterial lactase gene from dysbacterial diarrhea mice, as the good therapeutic mechanism of QWBZP on antibiotics-induced diarrhea. Dysbacterial diarrhea mice model was constructed by gastric perfusion with mixture of cephradine capsules and gentamicin sulfate (23.33 mL kg-1 day-1) for 5 days. After the success of establishing diarrhea, the mice in treatment group were gavaged with QWBZP for 3 days. Intestinal mucosa in each group was collected, and diversity of bacterial lactase genes in intestinal mucosa of mice was carried out by Miseq metagenome sequencing. The results showed the Chao1, ACE, Simpson and Shannon indices in treatment group were lower than model group and were similar to control group. The same result was obtained from the operational taxonomic units (OTUs). There were 298, 435 and 254 OTUs in the control group, model group and treatment group, respectively. Principal component analysis (PCA) indicated that samples distribution in both normal and treatment groups were relatively intensive, distances among individuals were small, while opposite results were observed in model group. Moreover, antibiotics increased the diversity and abundance of bacterial lactase genes at phylum and genus levels. However, they decreased and were similar to control group after treating with QWBZP. Our results indicate that QWBZP has a positive effect on the recovery of bacterial lactase gene diversity to normal level. In addition, QWBZP increase the abundance of Lysobacter and Eukaryota.

Bacterial lactase genes diversity in intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics.

The current study aimed at exploring the diversity of bacterial lactase genes in the intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics and to provide experimental basis for antibiotics-induced diarrhea. Mice model of dysbacterial diarrhea was established by gastric perfusion with mixture of cephradine capsules and gentamicin sulfate (23.33 mL kg-1 d-1), twice a day and continuously for 5 days. Intestinal mucosa from jejunum to ileum was collected, and bacterial metagenomic DNA was extracted for Miseq metagenome sequencing to carry out diversity analysis. The results showed that specific operational taxonomic units (OTUs) were 45 in the control group and 159 in the model group. The Chao1, ACE, Shannon and Simpson indices in model group were significantly higher (P < 0.01 or P < 0.05) than control group. Principal component analysis (PCA) and box chart of the control group were relatively intensive, while in the model group, they were widely dispersed. Furthermore, the inter-group box area was higher than that in the intra-group. Compared with the model group, the abundance of bacterial lactase genes in Proteobacteria from the intestinal mucosa of the control group was higher, but lower in Actinobacteria and unclassified bacteria. At the genus level, the relative abundance of bacterial species and taxon units in model group was obviously increased (P < 0.05). Our results indicate that antibiotics increased the diversity and abundance of bacterial lactase genes in the intestinal mucosa, as the abundance of Betaproteobacteria, Cupriavidus, Ewingella, Methyloversatilis, Rhodocyclaceae and Rhodocyclales. In addition, antibiotics become an additional source for lactase genes of Ewingella, Methyloversatilis, Mycobacterium, Microbacterium, Beutenberqia and Actinomyces.

Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea.

AIM: To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea. METHODS: Following 2 d of adaptive feeding, 12 specific pathogen-free Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics (23.33 mL·kg-1·d-1) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units (OTUs) was carried out after amplification and sequencing. RESULTS: OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups (P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively. CONCLUSION: Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.

Effects of Debaryomyces hansenii treatment on intestinal microorganisms in mice with antibiotics-induced diarrhea.

To investigate the influence of Debaryomyces hansenii treatment on intestinal microorganisms in mice with antibiotics-induced diarrhea, mouse model of antibiotics-induced diarrhea was created by gavaging mice with mixed antibiotics (23.33 mL/kg/days) composed of gentamycin sulfate and cefradine for 5 days. Mice with the symptom of diarrhea were then treated with D. hansenii by intragastric administration. The control group mice were given with sterile water. After 4 day treatment, total DNA of intestinal microflora of treated and control mice was extracted, and their quantities were measured by sequencing the V4 region of 16S rDNA. The results showed that when compared to the control (sterile water), treatment with D. hansenii increased the operational taxonomic units (OTUs) of intestinal bacteria. The Chao index in diarrhea treated group was higher than diarrhea control group and was similar to healthy control group, while all differences had no significance (P > 0.05). D. hansenii treatment increased the Shannon index but not significantly (P > 0.05). Moreover, there was not significant impact on density and diversity of intestinal bacterial population at phylum and genus levels (P > 0.05). Interestingly, D. hansenii treatment recovered the population density of certain bacterium species, such as Bacteroidaceae (in family level) (P < 0.05). Our results indicate that D. hansenii has potency of adjusting the density and diversity of intestinal bacteria and recovering the population density of Bacteroidaceae in family level.