L. pseudomesenteroides and L. johnsonii isolated from yaks in Tibet modulate gut microbiota in mice to ameliorate enteroinvasive Escherichia coli-induced diarrhea

Metagenomic Analysis Reveals A Gut Microbiota Structure and Function Alteration between Healthy and Diarrheic Juvenile Yaks

Diarrhea-induced mortality among juvenile yaks is highly prevalent in the pastoral areas of the Qinghai-Tibet plateau. Although numerous diseases have been linked to the gut microbial community, little is known about how diarrhea affects the gut microbiota in yaks. In this work, we investigated and compared changes in the gut microbiota of juvenile yaks with diarrhea. The results demonstrated a considerable drop in the alpha diversity of the gut microbiota in diarrheic yaks, accompanied by Eysipelatoclostridium, Parabacteroides, and Escherichia-Shigella, which significantly increased during diarrhea. Furthermore, a PICRust analysis verified the elevation of the gut-microbial metabolic pathways in diarrhea groups, including glycine, serine, and threonine metabolism, alanine, aspartate, oxidative phosphorylation, glutamate metabolism, antibiotic biosynthesis, and secondary metabolite biosynthesis. Taken together, our study showed that the harmful bacteria increased, and beneficial bacteria decreased significantly in the gut microbiota of yaks with diarrhea. Moreover, these results also indicated that the dysbiosis of the gut microbiota may be a significant driving factor of diarrhea in yaks.

MTTLm6A: A multi-task transfer learning approach for base-resolution mRNA m6A site prediction based on an improved transformer

N6-methyladenosine (m6A) is a crucial RNA modification involved in various biological activities. Computational methods have been developed for the detection of m6A sites in Saccharomyces cerevisiae at base-resolution due to their cost-effectiveness and efficiency. However, the generalization of these methods has been hindered by limited base-resolution datasets. Additionally, RMBase contains a vast number of low-resolution m6A sites for Saccharomyces cerevisiae, and base-resolution sites are often inferred from these low-resolution results through post-calibration. We propose MTTLm6A, a multi-task transfer learning approach for base-resolution mRNA m6A site prediction based on an improved transformer. First, the RNA sequences are encoded by using one-hot encoding. Then, we construct a multi-task model that combines a convolutional neural network with a multi-head-attention deep framework. This model not only detects low-resolution m6A sites, it also assigns reasonable probabilities to the predicted sites. Finally, we employ transfer learning to predict base-resolution m6A sites based on the low-resolution m6A sites. Experimental results on Saccharomyces cerevisiae m6A and Homo sapiens m1A data demonstrate that MTTLm6A respectively achieved area under the receiver operating characteristic (AUROC) values of 77.13% and 92.9%, outperforming the state-of-the-art models. At the same time, it shows that the model has strong generalization ability. To enhance user convenience, we have made a user-friendly web server for MTTLm6A publicly available at http://47.242.23.141/MTTLm6A/index.php.

The Effects of Lactobacillus johnsonii on Diseases and Its Potential Applications

Lactobacillus johnsonii has been used as a probiotic for decades to treat a wide range of illnesses, and has been found to have specific advantages in the treatment of a number of ailments. We reviewed the potential therapeutic effects and mechanisms of L. johnsonii in various diseases based on PubMed and the Web of Science databases. We obtained the information of 149 L. johnsonii from NCBI (as of 14 February 2023), and reviewed their comprehensive metadata, including information about the plasmids they contain. This review provides a basic characterization of different L. johnsonii and some of their potential therapeutic properties for various ailments. Although the mechanisms are not fully understood yet, it is hoped that they may provide some evidence for future studies. Furthermore, the antibiotic resistance of the various strains of L. johnsonii is not clear, and more complete and in-depth studies are needed. In summary, L. johnsonii presents significant research potential for the treatment or prevention of disease; however, more proof is required to justify its therapeutic application. An additional study on the antibiotic resistance genes it contains is also needed to reduce the antimicrobial resistance dissemination.

Gut microbiota bridges the iron homeostasis and host health

The gut microbiota acts as a symbiotic microecosystem that plays an indispensable role in the regulation of a number of metabolic processes in the host by secreting secondary metabolites and impacting the physiology and pathophysiology of numerous organs and tissues through the circulatory system. This relationship, referred to as the "gut-X axis", is associated with the development and progression of disorders, including obesity, fatty liver and Parkinson's disease. Given its importance, the gut flora is a vital research area for the understanding and development of the novel therapeutic approaches for multiple disorders. Iron is a common but necessary element required by both mammals and bacteria. As a result, iron metabolism is closely intertwined with the gut microbiota. The host's iron homeostasis affects the composition of the gut microbiota and the interaction between host and gut microbiota through various mechanisms such as nutrient homeostasis, intestinal peaceability, gut immunity, and oxidative stress. Therefore, understanding the relationship between gut microbes and host iron metabolism is not only of enormous significance to host health but also may offer preventative and therapeutic approaches for a number of disorders that impact both parties. In this review, we delve into the connection between the dysregulation of iron metabolism and dysbiosis of gut microbiota, and how it contributes to the onset and progression of metabolic and chronic diseases.

Dynamic changes of gut fungal community in horse at different health states

Accumulating studies indicated that gut microbial changes played key roles in the progression of multiple diseases, which seriously threaten the host health. Gut microbial dysbiosis is closely associated with the development of diarrhea, but gut microbial composition and variability in diarrheic horses have not been well characterized. Here, we investigated gut fungal compositions and changes in healthy and diarrheic horses using amplicon sequencing. Results indicated that the alpha and beta diversities of gut fungal community in diarrheal horses changed significantly, accompanied by distinct changes in taxonomic compositions. The types of main fungal phyla (Neocallimastigomycota, Ascomycota, and Basidiomycota) in healthy and diarrheal horses were same but different in relative abundances. However, the species and abundances of dominant fungal genera in diarrheal horses changed significantly compared with healthy horses. Results of Metastats analysis indicated that all differential fungal phyla (Blastocladiomycota, Kickxellomycota, Rozellomycota, Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Glomeromycota, and Olpidiomycota) showed a decreasing trend during diarrhea. Moreover, a total of 175 differential fungal genera were identified for the gut fungal community between healthy and diarrheal horses, where 4 fungal genera increased significantly, 171 bacterial genera decreased dramatically during diarrhea. Among these decreased bacteria, 74 fungal genera even completely disappeared from the intestine. Moreover, this is the first comparative analysis of equine gut fungal community in different health states, which is beneficial to understand the important role of gut fungal community in equine health.

Pesticide thiram exposure alters the gut microbial diversity of chickens

Thiram is a major dithiocarbamate pesticide commonly found in polluted field crops, feed, and rivers. Environmental thiram exposure has been demonstrated to cause angiogenesis and osteogenesis disorders in chickens, but information regarding thiram influences on gut microbiota, apoptosis, and autophagy in chickens has been insufficient. Here, we explored the effect of thiram exposure on gut microbiota, apoptosis, and autophagy of chickens. Results demonstrated that thiram exposure impaired the morphology and structure of intestinal and liver tissues. Moreover, thiram exposure also triggered liver apoptosis and autophagy. The gut microbiota in chickens exposed to thiram exhibited a significant decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Bacterial taxonomic analysis indicated that thiram exposure causes a significant reduction in the levels of eight genera, as well as a significant increase in the levels of two phyla and 10 genera. Among decreased bacterial genera, seven genera even cannot be observed in the thiram-induced chickens. In summary, this study demonstrated that thiram exposure not only dramatically altered the gut microbial diversity and composition but also induced liver apoptosis and autophagy in chickens. Importantly, this study also conveyed a key message that the dysbiosis of gut microbiota may be one of the major pathways for thiram to exert its toxic effects.

Integrated Bacteria-Fungi Diversity Analysis Reveals the Gut Microbial Changes in Buffalo With Mastitis

The gut microbial community is closely related to mastitis, but studies regarding the influences of mastitis on gut microbiota in buffalo remain scarce. Herein, we characterized the differences in gut bacterial and fungal communities between mastitis-affected and healthy buffalos. Interestingly, although mastitis had no effect on gut bacterial and fungal diversities in the buffalos, some bacterial and fungal taxa were significantly altered. Bacterial and fungal taxonomic analysis showed that the preponderant bacterial phyla (Firmicutes and Bacteroidetes) and fungal phyla (Ascomycota and Basidiomycota) in buffalo were the same regardless of health status. At the level of genus, the changes in some gut bacterial and fungal abundances between both groups were gradually observed. Compared with healthy buffalos, the proportions of 3 bacterial genera (uncultured_bacterium_f_Muribaculaceae, Eubacterium_nodatum_group, and Lachnoclostridium_10) and 1 fungal genus (Pichia) in the mastitis-affected buffalo were significantly increased, whereas 4 bacterial genera (Ruminococcus_2, Candidatus_Stoquefichus, Turicibacter, and Cellulosilyticum) and 4 fungal genera (Cladosporium, Thermothelomyces, Ganoderma and Aspergillus) were significantly decreased. Taken together, this research revealed that there was significant difference in the compositions of the gut microbial community between the healthy and mastitis-affected buffalos. To our knowledge, this is the first insight into the characteristics of the gut microbiota in buffalos with mastitis, which is beneficial to understand the gut microbial information of buffalo in different health states and elucidate the pathogenesis of mastitis from the gut microbial perspective.

Comparative analysis of gut microbiota in healthy and diarrheic yaks

BACKGROUND

Yak (Bos grunniens) mainly inhabiting Tibet Plateau, displayed a high incidence of diarrhea due to harsh living environment and nutritional deficit. Gut microbial community has been reported to be closely related to many diseases including diabetes, obesity and inflammatory bowel disease, but information regarding diarrheic influence on gut microbiota in yaks remains scarce. Here, this study was performed to investigate the gut bacterial and fungal alternations of diarrheic yaks.

RESULTS

Results revealed that the gut bacterial and fungal communities of diarrheic yaks showed a distinct decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Specifically, diarrhea caused a distinct increase in the relative abundance of 1 phylum and 8 genera as well as a distinct decrease in 3 phyla and 30 genera. Fungal taxonomic analysis indicated that the relative richness of 1 phylum and 2 genera dramatically increased, whereas the relative richness of 2 phylum and 43 genera significantly decreased during diarrhea. Surprisingly, 2 bacterial genera and 5 fungal genera even cannot be detected in the gut microbiota of diarrheic yaks.

CONCLUSIONS

In summary, this study indicated that the gut bacterial and fungal compositions and diversities of yaks altered significantly during diarrhea. Moreover, these findings also contribute to understanding the gut microbial composition and diversity of yaks and developing strategies to alleviate and prevent diarrhea from gut microbial perspective.

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses

Increasing evidence reveals the importance of gut microbiota in animals for regulating intestinal homeostasis, metabolism, and host health. The gut microbial community has been reported to be closely related to many diseases, but information regarding diarrheic influence on gut microbiota in horses remains scarce. This study investigated and compared gut microbial changes in horses during diarrhea. The results showed that the alpha diversity of gut microbiota in diarrheic horses decreased observably, accompanied by obvious shifts in taxonomic compositions. The dominant bacterial phyla (Firmicutes, Bacteroidetes, Spirochaetes, and Kiritimatiellaeota) and genera (uncultured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_p-251-o5, Lachnospiraceae_AC2044_group, and Treponema_2) in the healthy and diarrheic horses were same regardless of health status but different in abundances. Compared with the healthy horses, the relative abundances of Planctomycetes, Tenericutes, Firmicutes, Patescibacteria, and Proteobacteria in the diarrheic horses were observably decreased, whereas Bacteroidetes, Verrucomicrobia, and Fibrobacteres were dramatically increased. Moreover, diarrhea also resulted in a significant reduction in the proportions of 31 genera and a significant increase in the proportions of 14 genera. Taken together, this study demonstrated that the gut bacterial diversity and abundance of horses changed significantly during diarrhea. Additionally, these findings also demonstrated that the dysbiosis of gut microbiota may be an important driving factor of diarrhea in horses.

Alterations in the Gut Microbial Composition and Diversity of Tibetan Sheep Infected With Echinococcus granulosus

Hydatidosis/cystic echinococcosis (CE) caused by Echinococcus granulosus is a parasitic zoonotic disease worldwide, threatening animal health and production and public health safety. However, it is still unclear that whether E. granulosus infection can result in the alteration of gut microbiota in Tibetan sheep. Therefore, a study was designed to investigate the influences of E. granulosus infection on gut microbiota of Tibetan sheep. A total of 10 ovine small intestinal contents (five from healthy and five from infected) were obtained and subjected to high-throughput sequencing by MiSeq platform. A total of 2,395,641 sequences and 585 operational taxonomic units (OTUs) were identified. Firmicutes and Proteobacteria were the most dominant phyla in all samples. Moreover, the proportions of Armatimonadetes and Firmicutes in the infected Tibetan sheep were significantly decreased, whereas Actinobacteria, Chloroflexi, and Acidobacteria had significantly increased. At the genus level, the Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group were the predominant bacterial genera in all the samples. Furthermore, the healthy Tibetan sheep exhibited higher abundances of Intestinimonas, Butyrivibrio, Pseudobutyrivibrio, Ruminococcaceae, Eubacterium_coprostanoligenes_group, Oxobacter, Prevotella_1, Ruminiclostridium_6, Coprococcus_1, Ruminococcus, Lachnospiraceae_UCG-002, Olsenella, and Acetitomaculum, whereas Kocuria, Clostridium_sensu_stricto_1, Slackia, Achromobacter, and Stenotrophomonas levels were lower. In conclusion, our results conveyed an information that E. granulosus infection may cause an increase in pathogenic bacteria and a decrease in beneficial bacteria. Additionally, a significant dynamical change in gut microbiota could be associated with E. granulosus infection.

Environmental hexavalent chromium exposure induces gut microbial dysbiosis in chickens

Hexavalent chromium [Cr (VI)] is a hazardous heavy metal that pollutes soil, water and crops. Moreover, its prolonged exposure can harm the gastrointestinal system, liver and respiratory tract in different species, but knowledge regarding Cr (VI) influence on gut microbiota in chickens remains scarce. Therefore, this study was performed to investigate the impact of Cr (VI) on gut microbiota in chickens. Results revealed that the gut microbiota in Cr (VI)-induced chickens exhibited a distinct reduction in alpha diversity, accompanied by significant shifts in microbial composition. Specifically, Firmicutes and Bacteroidetes were the most dominant phyla in the control chickens, whereas Firmicutes and Actinobacteria were observed to be predominant in the Cr (VI)-induced populations. Moreover, the types and relative abundances of predominant bacterial genus in control and Cr (VI)-induced chickens were also different. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla and 7 genera obviously increased, whereas 8 phyla and 30 genera dramatically decreased during Cr (VI) induction. Among them, 1 phylum (Deferribacteres) and 5 genera (Butyricicoccus, Butyricimonas, Intestinimonas, Lachnospiraceae_FCS020_group and Ruminococcaceae_V9D2013_group) even could not be found in the gut microbial community of Cr (VI)-induced chickens. Taken together, our study indicated that the long-term exposure to Cr (VI) dramatically alter the gut microbial diversity and composition in chickens. Notably, it represents a breakthrough in understanding the impact of Cr (VI) on the intestinal microbiota of chickens.

Dynamic distribution of nasal microbial community in yaks (Bos grunniens) at different ages

The significance of microbial community structure has been extensively recognized due to its key roles in metabolism, immunity, and health maintenance. Importantly, increasing evidence indicated that the dynamic distribution of microbial community structure can be used for evaluating the health condition of host. Yaks (Bos grunniens), mainly inhabiting in high-altitude hypoxic environment, are characterized by excellent adaptability and strong resistance. Currently, it has been determined that yaks possessed the complicated gastrointestinal microbial ecosystem, whereas not much is known about the nasal microbial community structure of yaks. Therefore, this study was performed to compare and analyze the differences in nasal microbiota of yaks with different ages by high-throughput sequencing. In this study, a total of 487,168 and 486,498 high-quality sequences were achieved from YYG (1-month-old yaks) and AYG (1-year-old yaks), respectively. Additionally, 5,340 operational taxonomic units (OTUs) were identified and 657 OTUs were in common among all samples. Proteobacteria and Firmicutes were the two most predominant phyla in all samples. Moreover, Actinobacteria and Bacteroidetes were the tertiary dominant phyla in YYG and AYG, respectively. At the level of genus, Moraxella, Faucicola, and Mannheimia were the most preponderant bacterial genera in the young and adult yaks. As compared to the AYG, the proportions of Actinobacillus, Parabacteroides, and Haemophilus in the YYG were significantly increased, whereas the Rhizobacter was decreased. In conclusion, this study firstly compared and investigated the distribution of nasal microbiota in yaks with different ages. Results demonstrated that age was an important factor affecting the nasal microbiota. Moreover, the current study will provide a theoretical basis for the further study on the microbial community structure of yaks.

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes

Gut microbiota has been demonstrated to be associated with multiple gastrointestinal diseases, but information regarding the gut microbial alternations in diarrheic giraffe remains scarce. Here, 16S rDNA and ITS gene amplicon sequencing were conducted to investigate the gut microbial composition and variability in diarrheic giraffes. Results demonstrated that Firmicutes and Proteobacteria were the most dominant phyla in the gut bacterial community, whereas Ascomycota and Basidiomycota were observed to be predominant in the gut fungal community regardless of health status. However, the species and relative abundance of preponderant bacterial and fungal genera in healthy and diarrheic giraffes were different. In contrast to the relatively stabilized gut fungal community, gut bacterial community displayed a significant decrease in the alpha diversity, accompanied by distinct changes in taxonomic compositions. Bacterial taxonomic analysis revealed that the relative abundances of eight phyla and 12 genera obviously increased, whereas the relative abundances of two phyla and eight genera dramatically decreased during diarrhea. Moreover, the relative richness of five fungal genera significantly increased, whereas the relative richness of seven fungal genera significantly declined in diarrheic giraffes. Taken together, this study demonstrated that diarrhea could cause significant alternations in the gut microbial composition of giraffes, and the changes in the gut bacterial community were more significant than those in the gut fungal community. Additionally, investigating the gut microbial characteristics of giraffes in different health states is beneficial to provide a theoretical basis for establishing a prevention and treatment system for diarrhea from the gut microbial perspective.

Association of gut microbiomes with lung and esophageal cancer: a pilot study

Gut microbiota, especially human pathogens, has been shown to be involved in the occurrence and development of cancer. Esophageal squamous cell carcinoma and lung cancer are two malignant cancers, and their relationship with gut microbiota is still unclear. Virulence factor database (VFDB) is an integrated and comprehensive online resource for curating information about human pathogens. Here, based on VFDB database, we analyzed the differences of bacteria at genus level in the gut of patients with esophageal squamous cell carcinoma, lung cancer, and healthy controls. We proposed the possible cancer-associated bacteria in gut and put forward their possible effects. Apart from this, principal coordinate analysis (PCoA) and analysis of similarities (ANSOIM) suggested that some bacteria in the gut can be used as potential biomarkers to screen esophageal squamous cell carcinoma and lung cancer, and their effectiveness was preliminary verified. The relative abundance of Klebsiella and Streptococcus can be used to distinguish patients with esophageal squamous cell carcinoma and lung cancer from healthy controls. The absolute abundance of Klebsiella can further distinguish patients with esophageal squamous cell carcinoma from patients with lung cancer. In particular, the relative abundance of Fusobacterium can directly distinguish between patients with esophageal squamous cell carcinoma and healthy controls. Additionally, the absolute abundance of Haemophilus can distinguish lung cancer from healthy controls. Our study provided a new way based on VFDB database to explore the relationship between gut microbiota and cancer, and initially proposed a feasible cancer screening method.

Microbiome analysis reveals the significant changes in gut microbiota of diarrheic Baer's Pochards (Aythya baeri)

Gut microbiota has been demonstrated to play multiple crucial roles in immunity, physiology, metabolism, and health maintenance. Diarrhea was closely related to the gut microbiota, but information regarding the alterations in gut microbial composition and structure in Baer's Pochard (Aythya baeri) with diarrhea remains scarce. Here, 16S rDNA amplicon sequencing was performed to investigate the gut microbial variability between diarrheic and healthy Baer's Pochard. Results indicated that the gut bacterial community of diarrheic Baer's Pochard showed a distinct decrease in alpha diversity, accompanied by evident changes in taxonomic compositions. Microbial taxonomic analysis revealed that Firmicutes, Proteobacteria and Bacteroidetes were the most dominant phyla in all the fecal samples regardless of health status. At the genus level, the differences in gut bacterial abundance between healthy and diarrheic populations were gradually observed. Specifically, the proportion of Elusimicrobia in the diarrheic Baer's Pochard was increased in comparison with healthy populations, while Acidobacteria, Rokubacteria, Cyanobacteria and Patescibacteria were dramatically decreased. Additionally, the relative proportion of 23 bacterial genera significantly decreased in diarrheic Baer's Pochard, whereas the relative percentage of 4 bacterial genera (Alkanindiges, Elusimicrobium, Spirosoma and Exiguobacterium) observably increased as compared to healthy populations. Taken together, the present study revealed that there were distinct differences in the gut microbial composition and diversity between the healthy and diarrheic Baer's Pochard. Remarkably, this is the first report on the differences in the gut microbiota of Baer's Pochard under different health states and may contribute to provide better insight into gut microbial composition and diversity of Baer's Pochard.

Microbiome Analysis Reveals the Dynamic Alternations in Gut Microbiota of Diarrheal Giraffa camelopardalis

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

Microbiome analysis reveals the alterations in gut microbiota in different intestinal segments of Yimeng black goats

Mounting evidence revealed the importance of gut microbiota in host metabolism, immunity and physiology, and health. Yimeng black goats (YBGs) mainly distributed in Shandong province of China, displayed a complicated intestinal microecosystem, but studies of its gut microbiota are still insufficient to report. Therefore, this study was performed with an objective to characterize the intestinal microbial community structure and diversity in the small intestine (duodenum, jejunum and ileum) and cecum of YBGs and investigated the variability of gut microbiota of different intestinal segments. A total of 12 intestinal samples were collected from YBGs for high-throughput sequencing analysis based on V3-V4 variable region of 16S rRNA genes. Our results revealed alterations in gut microbial composition with obvious differences in relative abundance between the different intestinal segments. Additionally, small intestine including duodenum, jejunum and ileum not only displayed higher species abundance and diversity than cecum but also showed a significant difference among the main components of gut microbiota based on the analytical results of alpha and beta diversities. At the phylum level, Firmicutes and Proteobacteria were the most preponderant phyla in all the samples regardless of intestinal sites. Moreover, the microbiota in small intestine was significantly different from cecum, which were characterized by the higher relative abundance of Butyrivibrio_2, Megasphaera, Halomonas, Delftia, Hydrogenophaga, Limnobacter, Pseudoxanthomonas, Novosphingobium, Janibacter and Erythrobacter, whereas the levels of Butyricicoccus, unidentified_Lachnospiraceae, Fusicatenibacter, Akkermansia, Ruminococcaceae_NK4A214_group and Lactobacillus were lower. Overall, this study first characterized the profile of gut microbiota composition in different intestinal sites and provide better insight into intestinal microbial community structure and diversity of YBGs.

L. johnsonii, L. plantarum, and L. rhamnosus alleviated Enterohaemorrhagic Escherichia coli-induced diarrhoea in mice by regulating gut microbiota

Enterohaemorrhagic Escherichia coli (EHEC) is a prominent foodborne pathogen that causes infectious intestinal diarrhoea. Lactobacillus is a recognized probiotic that inhibits intestinal pathogens and maintains the balance of the intestinal flora. The purpose of this study was to investigate the regulatory effects of three Lactobacillus strains, L. johnsonii, L. plantarum, and L. rhamnosus, on the intestinal flora of EHEC-infected mice. The initial weight and diarrhoea index of the mice were recorded. After 21 days, the faeces of the mice were subjected to 16S rDNA high-throughput sequencing. The diarrhoea index of mice treated with Lactobacillus improved, their body weight continued to rise, and their liver index gradually decreased. The α diversity analysis showed that the intestinal flora diversity and abundance were lower in mice infected with EHEC than in healthy mice. L. plantarum, L. johnsonii, and L. rhamnosus significantly improved the diversity of the flora species. In terms of flora composition, the three main phyla present were Bacteroidetes, Firmicutes, and Proteobacteria. The abundance of these three phyla was reduced to 93.81% after infection and restored to over 96.30% after treatment. At the genus level, Lactobacillus reduced the abundance of Bacteroides, Helicobacter pylori, and Shigella, while increasing the abundance of butyric acid-producing bacteria and Lactobacillus. Finally, a heat map and non-metric multidimensional scaling analysis showed that the intestinal flora structures in the L. johnsonii, L. plantarum, and L. rhamnosus treatment groups were closest to those of healthy mice. In conclusion, L. johnsonii, L. plantarum, and L. rhamnosus regulated and improved the structure of intestinal flora and relieved diarrhoea caused by EHEC infection.

The in vitro Effects of the Probiotic Strain, Lactobacillus casei ZX633 on Gut Microbiota Composition in Infants With Diarrhea

We investigated the in vitro effects of Lactobacillus casei ZX633 on gut microorganism composition in infants with diarrhea. For this purpose, 103 feces samples from healthy infants (healthy group) and 300 diarrhea samples from infants (diarrhea group) were collected, and diarrhea feces were treated with L. casei ZX633, which was previously isolated from healthy infant feces (treatment group). We used microbial dilution plate methods, high performance liquid chromatography (HPLC) and high-throughput sequencing approaches to analyze viable main microorganism counts, short chain fatty acid (SCFA) concentrations, and intestinal microbiota composition in feces, respectively. Our data showed that L. casei ZX633 supplementation increased the numbers of Escherichia coli, yeasts, lactic acid bacteria (LAB) and aerobic-bacteria, raised propionic acid levels but reduced four other SCFAs, which are close to the healthy group. Alpha diversity results indicated that microbial diversity and richness decreased in treatment group. Bacterial community analyses revealed that microbial structures of the treatment group tended toward the healthy group; i.e., Escherichia-Shigella and Clostridioides abundance increased, and there was a reduction in the abundance of Streptococcus, Bacteroides, Enterococcus and Veillonella. In conclusion, L. casei ZX633 isolated from healthy infant feces, may be effective in improving infant diarrhea microbiota, potentially providing a new probiotic strain to reduce the incidence of diarrhea associated with bacterial disease in infants.

Recombinant invasive Lactobacillus plantarum expressing the Eimeria tenella fusion gene TA4 and AMA1 induces protection against coccidiosis in chickens

Coccidiosis is an intestinal parasitic disease that is caused by Eimeria tenella and other species, and it seriously restricts the economic development of the broiler breeding industry. In this study, a recombinant Lactobacillus plantarum with an invasive effect was constructed, and it expressed the TA4-AMA1 protein of E. tenella. After oral immunization with recombinant L. plantarum, specific humoral and mucosal immune levels were measured by indirect ELISA, and the differentiation of T cells was analysed by flow cytometry. After challenge with sporulated oocysts, the body weight, oocyst shedding and cecum lesions of the chicken were evaluated. The results indicated that chickens immunized with recombinant invasive L. plantarum produced higher levels of specific antibodies in the serum than did the non-immunized controls, and the secretory IgA (sIgA) levels were increased in the intestinal washes compared to those of the controls (P < 0.05). Flow cytometry showed that recombinant invasive L. plantarum significantly stimulated T cell differentiation compared to the PBS group (P < 0.01, P < 0.001), and a higher proportion of CD4⁺ and CD8⁺ T cells were detected in peripheral blood. Moreover, the lesion scores and histopathological caecum sections showed that immunizing chickens with recombinant invasive L. plantarum can significantly relieve pathological damage in the cecum (P < 0.01), and the relative body weight gain was 89.64 %, which was higher than the 79.83 % gain in the chickens immunized with non-invasive L. plantarum. After the challenge, faeces from ten chickens in each group were collected between 4 and 7 days, and the oocysts per gram (OPG) was determined by the McMaster technique. The data indicated that oocysts in the faeces of chickens immunized with the recombinant invasive L. plantarum were significantly lower than those of the controls (P < 0.01). The results suggest that recombinant invasive L. plantarum effectively activated immune responses against E. tenella infection and can be used as a candidate vaccine against E. tenella infection.

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

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

Probiotic potential of Lactobacillus on the intestinal microflora against Escherichia coli induced mice model through high-throughput sequencing

The aim of this study was to evaluate the antibacterial potential of Lactobacillus screened from Tibetan yaks on clinical symptoms and intestinal microflora in enteroinvasive Escherichia coli (EIEC) induced mice model. In vitro study, Lactobacillus reuteri (LR1) exhibited stronger resistance to acid and bile and inhibited the growth of EIEC than Lactobacillus mucosae (LM1). The mice were randomly divided into four groups i.e. the LR1 group (LR1 1 × 10⁹ CFU/day), LM1 group (LM1 1 × 10⁹ CFU/day), blank control group and control group. Mice in control, LR1, and LM1 groups were challenged with EIEC on day 23. The body weight in the control and LM1 groups were significantly decreased after the infection with EIEC (P < 0.05), whereas the body weight of mice in the LR1 group did not change significantly (P > 0.05). The lowest diarrhea rate was recorded in the LR1 group after infection with EIEC. The results showed that the number of pathogens in the control group was higher than that in the experimental groups. The sequence analysis and OTU classification showed that the duodenum, ileum, and cecum of mice in the LR1 group had the highest number of OTUs compared with other groups. Whereas, the diversity analysis showed that in duodenum, ileum and cecum of mice in the LR1 group had the highest abundance and diversity. The composition of intestinal microbes indicated the presence of high proportions of Firmicutes, Proteobacteria and Bacteroidetes. Heat map analysis indicated high abundance of Bdello vibrio in the duodenum of mice in the LR1 group, while many pathogens were found in the different part of intestines in the control group, such as Streptococcus, Clostridium and Pseudomonas. In conclusion, pre-supplementation of LR1 alleviate the clinical symptoms caused by E. coli, and promote a healthy gut flora.

Influence of dietary supplementation with Bacillus velezensis on intestinal microbial diversity of mice

Yaks are an aboriginal breed of the Qinghai-Tibet plateau (3000 m), which are highly adaptable to cold and hypoxic environments. It is noticed that hypoxia and hypothermia can induce changes in intestinal microbial structure in animals. Increasing evidences suggested that probiotics supplementation can improve the balance of gut microbiota of animals. However, so far, very few studies have emphasized on the probiotics isolated from yaks in the Qinghai-Tibet Plateau. Therefore, a potential probiotic strain Bacillus velezensis was isolated from yaks. In the present study, a total of 18 Kunming mice (15-18 g) were equally distributed into two groups; control and probiotic treated groups (1 × 10⁹ CFU/day). During the experimental period, all the mice from both groups were given standard normal diet ad libitum. At the end of the experiment, mice were euthanized and the intestines (duodenum, jejunum, ileum, and cecum) were removed for high-throughput sequencing. The results demonstrated that Bacillus velezensis supplementation showed beneficial effects on the gut microbiota of mice. Specifically, Bacillus velezensis supplementation increased the population of Lactobacillus and Ruminococcus in the duodenum, and Candidatus Arthromitus in the jejunum. Additionally, Acinetobacter in the duodenum and Helicobacter in the cecum were decreased after feeding Bacillus velezensis. Altogether, these findings suggested that Bacillus velezensis isolated from Tibetan yaks can improve gut microbiota of mice.