Pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data

Maternal short chain fructo-oligosaccharides supplementation during late gestation and lactation influences milk components and offspring gut metabolome: a pilot study

Breast milk composition is influenced by maternal diet. This study aimed to evaluate if supplementation of maternal diet with a prebiotic fibre, through its potential effect on milk composition, can be a leverage to orientate the gut microbiota of infants in a way that would be beneficial for their health. Twelve sows received a diet supplemented with short chain fructo-oligosaccharides or maltodextrins during the last month of gestation and the lactation. Oligosaccharidic and lipidomic profiles of colostrum and mature milk (21 days), as well as faecal microbiota composition and metabolomic profile of 21 day-old piglets were evaluated. The total porcine milk oligosaccharide concentration tended to be lower in scFOS-supplemented sows, mainly due to the significant reduction of the neutral core oligosaccharides (in particular that of a tetrahexose). Maternal scFOS supplementation affected the concentration of 31 lipids (mainly long-chain triglycerides) in mature milk. Faecal short-chain fatty acid content and that of 16 bacterial metabolites were modified by scFOS supplementation. Interestingly, the integrative data analysis gave a novel insight into the relationships between (i) maternal milk lipids and PMOs and (ii) offspring faecal bacteria and metabolites. In conclusion, scFOS-enriched maternal diet affected the composition of mature milk, and this was associated with a change in the colonisation of the offspring intestinal microbiota.

Effect of different ways of ingesting orange essential oil on blood immune index and intestinal microflora in mice

BACKGROUND

Studies have found that the addition of plant essential oils to feed had a positive effect on intestinal microflora and immunity in mice. However, the effect of different ways of ingestion of orange essential oil on mice has seldom been reported. In the present study, we investigated the effects of ingestion of orange essential oil by gavage, sniffing and feeding on intestinal microflora and immunity in mice.

RESULTS

The results obtained showed that a low concentration of essential oil feeding significantly increased the spleen index of mice (P < 0.05). The effect of different ways of ingestion on the thymus index, immunoglobulin G and immunoglobulin M of mice was not significant (P > 0.05). High and medium concentrations of essential oil feeding increased the level of interleukin-2 in mice (P < 0.05). H⁺ K⁺ -ATPase activity was significantly increased in mice fed with gavage and different concentrations of essential oil feed compared to the control group (P < 0.05). The analysis of the results of the microflora in the cecum and colon of mice indicated that the medium concentration of essential oil feeding group and the sniffing group significantly changed the structure of the flora and increased the diversity of the intestinal microflora. All three essential oil ingestion methods increased the abundance of Bacteroidetes and Lactobacillus in the intestine of mice.

CONCLUSION

Compared with gavage and feeding, sniffing had a significant effect on immunoglobulins in mice. All the three ingestion methods could affect the intestinal microflora of mice and increase the abundance of Lactobacillus. © 2022 Society of Chemical Industry.

Intestinal mucin-type O-glycans: the major players in the host-bacteria-rotavirus interactions

Rotavirus (RV) causes severe diarrhea in young children and animals worldwide. Several glycans terminating in sialic acids (SAs) and histo-blood group antigens (HBGAs) on intestinal epithelial cell (IEC) surface have been recognized to act as attachment sites for RV. IECs are protected by the double layer of mucus of which O-glycans (including HBGAs and SAs) are a major organic component. Luminal mucins, as well as bacterial glycans, can act as decoy molecules removing RV particles from the gut. The composition of the intestinal mucus is regulated by complex O-glycan-specific interactions among the gut microbiota, RV and the host. In this review, we highlight O-glycan-mediated interactions within the intestinal lumen prior to RV attachment to IECs. A better understanding of the role of mucus is essential for the development of alternative therapeutic tools including the use of pre- and probiotics to control RV infection.

The Complex Interactions Between Rotavirus and the Gut Microbiota

Human rotavirus (HRV) is the leading worldwide cause of acute diarrhea-related death in children under the age of five. RV infects the small intestine, an important site of colonization by the microbiota, and studies over the past decade have begun to reveal a complex set of interactions between RV and the gut microbiota. RV infection can temporarily alter the composition of the gut microbiota and probiotic administration alleviates some symptoms of infection in vivo, suggesting reciprocal effects between the virus and the gut microbiota. While development of effective RV vaccines has offered significant protection against RV-associated mortality, vaccine effectiveness in low-income countries has been limited, potentially due to regional differences in the gut microbiota. In this mini review, we briefly detail research findings to date related to HRV vaccine cohorts, studies of natural infection, explorations of RV-microbiota interactions in gnotobiotic pig models, and highlight various in vivo and in vitro models that could be used in future studies to better define how the microbiota may regulate RV infection and host antiviral immune responses.

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19

All of humans and other mammalian species are colonized by some types of microorganisms such as bacteria, archaea, unicellular eukaryotes like fungi and protozoa, multicellular eukaryotes like helminths, and viruses, which in whole are called microbiota. These microorganisms have multiple different types of interaction with each other. A plethora of evidence suggests that they can regulate immune and digestive systems and also play roles in various diseases, such as mental, cardiovascular, metabolic and some skin diseases. In addition, they take-part in some current health problems like diabetes mellitus, obesity, cancers and infections. Viral infection is one of the most common and problematic health care issues, particularly in recent years that pandemics like SARS and COVID-19 caused a lot of financial and physical damage to the world. There are plenty of articles investigating the interaction between microbiota and infectious diseases. We focused on stimulatory to suppressive effects of microbiota on viral infections, hoping to find a solution to overcome this current pandemic. Then we reviewed mechanistically the effects of both microbiota and probiotics on most of the viruses. But unlike previous studies which concentrated on intestinal microbiota and infection, our focus is on respiratory system's microbiota and respiratory viral infection, bearing in mind that respiratory system is a proper entry site and residence for viruses, and whereby infection, can lead to asymptomatic, mild, self-limiting, severe or even fatal infection. Finally, we overgeneralize the effects of microbiota on COVID-19 infection. In addition, we reviewed the articles about effects of the microbiota on coronaviruses and suggest some new therapeutic measures.

Cryptosporidium parvum-Infected Neonatal Mice Show Gut Microbiota Remodelling Using High-Throughput Sequencing Analysis: Preliminary Results

BACKGROUND

During the last decade, the scientific community has begun to investigate the composition and role of gut microbiota in normal health and disease. These studies have provided crucial information on the relationship between gut microflora composition and intestinal parasitic infection, and have demonstrated that many enteric pathogen infections are associated with altered gut microflora composition. In this study, we investigated the effects of Cryptosporidium parvum infection (zoonotic protozoan affecting a large range of vertebrates) on both qualitative and quantitative composition of gut microbiota in a CD-1 neonatal mouse model.

METHODS

5-day-old neonate mice were experimentally infected with 10⁵Cryptosporidium parvum Iowa oocysts by oesophageal gavage. The intestinal microbiota of both infected (Cp+) and uninfected (Cp-) mice groups was examined by high-throughput sequencing of the bacterial 16S rDNA gene V3-V4 hypervariable region.

RESULTS

The most consistent change in the microbiota composition of Cp+ mice was the increased proportion of bacterial communities belonging to the Phylum Bacteroidetes. In contrast, the microbiota of Cp- mice was associated with increased proportions of several Firmicutes and Actinobacteria phyla members.

CONCLUSION

For the first time, our study provides evidence of an association between cryptosporidial infection and gut dysbiosis, thus contributing valuable knowledge to the as-yet little-explored field of Cryptosporidium-microbiota interactions in a neonatal mouse model.

A metagenome-wide association study of gut microbiota in asthma in UK adults

BACKGROUND

Asthma, one of the most common chronic respiratory disorders, is associated with the hyper-activation of the T-cell subset of adaptive immunity. The gut microbiota may be involved in the development of asthma through the production of short-chain fatty acids (SCFAs), exhibiting modulatory effects on Th. So, we performed a metagenome-wide association study (MWAS) of the fecal microbiota from individuals with asthma and healthy controls. And that was the first case to resolve the relationship between asthma and microbiome among UK adults.

RESULTS

The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. Faecalibacterium prausnitzii, Sutterella wadsworthensis and Bacteroides stercoris were depleted in cases, whereas Clostridiums with Eggerthella lenta were over-represented in individuals with asthma. Functional analysis shows that the SCFAs might be altered in the microbiota of asthma patients.

CONCLUSION

In all, the adult human gut microbiome of asthma patients is clearly different from healthy controls. The functional and taxa results showed that the change of asthma patients might related to SCFAs.

Exposure to Arsenite in CD-1 Mice during Juvenile and Adult Stages: Effects on Intestinal Microbiota and Gut-Associated Immune Status

Intestinal microbiota composition and gut-associated immune response can contribute to the toxicity of arsenic. We investigated the potential toxicity of short-term arsenic exposure on gut microbiome composition, intestinal immune status, microbial arsenic resistance gene, and arsenic metabolic profiles in adult and developmental stages of CD-1 mice. The potential toxicity of arsenite [As(III)] was determined for two life stages: (i) adult animals at 24 or 48 h after single gavage (0.05 mg/kg body weight [b.w.] [low dose], 0.1 mg/kg b.w. [medium dose], and 0.2 mg/kg b.w. [high dose]) and repeated exposure at 1 mg/liter for 8 days and (ii) postnatal day 10 (PND10) and PND21 after single gavage (0.05 mg/kg b.w.). Dose- and time-dependent responses in bacterial recovery/microbial composition were observed in adults after a single gavage. Repeated exposure caused a transient decrease in the recovery of intestinal bacteria, a shift in the bacterial population with abundance of arsenic resistance genes, and evidence for host metabolism of arsenite into less-reactive trivalent methylated species. Arsenic exposure in adult animals induced high levels of CC chemokines and of proinflammatory and anti-inflammatory cytokine secretion in intestine. Arsenic exposure at PND21 resulted in the development of distinct bacterial populations. Results of this study highlight significant changes in the intestinal microbiome and gut-associated immune status during a single or repeated exposure to arsenic in juvenile and adult animals. The data warrant investigation of the long-term effects of oral arsenic exposure on the microbiome and of immune system development and responses.IMPORTANCE Transformation of organic arsenic to toxic inorganic arsenic (iAs) is likely carried out by intestinal bacteria, and iAs may alter the viability of certain microbial populations. This study addressed the impact of arsenic exposure on intestinal microbiota diversity and host gut-associated immune mediators during early development or adulthood using scenarios of acute or repeated doses. During acute arsenic exposure, animals developed defense functions characterized by higher abundances of bacteria that are involved in arsenic resistance or detoxification mechanisms. Arsenite had a negative effect on the abundance of bacterial species that are involved in the conversion of protein to butyrate, which is an alternative energy source in the intestine. The intestinal mucosal immune cytokine profile reflected a mechanism of protection from arsenic toxicity.

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing

Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.

Garay C, Vandenplas Y, Moya A. Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment

Gut microbiota is closely related to acute infectious diarrhea, one of the leading causes of mortality and morbidity in children worldwide. Understanding the dynamics of the recovery from this disease is of clinical interest. This work aims to correlate the dynamics of gut microbiota with the evolution of children who were suffering from acute infectious diarrhea caused by a rotavirus, and their recovery after the administration of a probiotic, Saccharomyces boulardii CNCM I-745. The experiment involved 10 children with acute infectious diarrhea caused by a rotavirus, and six healthy children, all aged between 3 and 4 years. The children who suffered the rotavirus infection received S. boulardii CNCM I-745 twice daily for the first 5 days of the experiment. Fecal samples were collected from each participant at 0, 3, 5, 10, and 30 days after probiotic administration. Microbial composition was characterized by 16S rRNA gene sequencing. Alpha and beta diversity were calculated, along with dynamical analysis based on Taylor's law to assess the temporal stability of the microbiota. All children infected with the rotavirus stopped having diarrhea at day 3 after the intervention. We observed low alpha diversities in the first 5 days (p-value < 0.05, Wilcoxon test), larger at 10 and 30 days after probiotic treatment. Canonical correspondence analysis (CCA) showed differences in the gut microbiota of healthy children and of those who suffered from acute diarrhea in the first days (p-value < 0.05, ADONIS test), but not in the last days of the experiment. Temporal variability was larger in children infected with the rotavirus than in healthy ones. In particular, Gammaproteobacteria class was found to be abundant in children with acute diarrhea. We identified the microbiota transition from a diseased state to a healthy one with time, whose characterization may lead to relevant clinical data. This work highlights the importance of using time series for the study of dysbiosis related to diarrhea.

Modeling human enteric dysbiosis and rotavirus immunity in gnotobiotic pigs

Background

Rotavirus vaccines have poor efficacy in infants from low- and middle-income countries. Gut microbiota is thought to influence the immune response to oral vaccines. Thus, we developed a gnotobiotic (Gn) pig model of enteric dysbiosis to study the effects of human gut microbiota (HGM) on immune responses to rotavirus vaccination, and the effects of rotavirus challenge on the HGM by colonizing Gn pigs with healthy HGM (HHGM) or unhealthy HGM (UHGM). The UHGM was from a Nicaraguan infant with a high enteropathy score (ES) and no seroconversion following administration of oral rotavirus vaccine, while the converse was characteristic of the HHGM. Pigs were vaccinated, a subset was challenged, and immune responses and gut microbiota were evaluated.

Results

Significantly more rotavirus-specific IFN-γ producing T cells were in the ileum, spleen, and blood of HHGM than those in UHGM pigs after three vaccine doses, suggesting HHGM induces stronger cell-mediated immunity than UHGM. There were significant correlations between multiple Operational Taxonomic Units (OTUs) and frequencies of IFN-γ producing T cells at the time of challenge. There were significant positive correlations between Collinsella and CD8+ T cells in blood and ileum, as well as CD4+ T cells in blood, whereas significant negative correlations between Clostridium and Anaerococcus, and ileal CD8+ and CD4+ T cells. Differences in alpha diversity and relative abundances of OTUs were detected between the groups both before and after rotavirus challenge.

Conclusion

Alterations in microbiome diversity and composition along with correlations between certain microbial taxa and T cell responses warrant further investigation into the role of the gut microbiota and certain microbial species on enteric immunity. Our results support the use of HGM transplanted Gn pigs as a model of human dysbiosis during enteric infection, and oral vaccine responses.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0136-y) contains supplementary material, which is available to authorized users.

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome

Microbes have co-evolved with human beings for millions of years. They play a very important role in maintaining the health of the host. With the advancement in next generation sequencing technology, the microbiome profiling in the host can be obtained under different circumstances. This review focuses on the current knowledge of the alteration of complex microbial communities upon the infection of different pathogens, such as human immunodeficiency virus, hepatitis B virus, influenza virus, and Mycobacterium tuberculosis, at different body sites. It is believed that the increased understanding of the correlation between infectious disease and the alteration of the microbiome can contribute to better management of disease progression in the future. However, future studies may need to be more integrative so as to establish the exact causality of diseases by analyzing the correlation between microorganisms within the human host and the pathogenesis of infectious diseases.

Oral antibiotic treatment induces skin microbiota dysbiosis and influences wound healing

Antibiotic treatment eliminates commensal bacteria and impairs mucosal innate immune defenses in the gut. However, whether oral antibiotic treatment could alter the composition of the microbiota on the skin surface and influence innate immune responses remains unclear. To test this, mice were treated with vancomycin for 7 days and then wounds were made on the back skin of the mice. Five days later, scar tissue from each mouse was collected for bacterial enumeration, the bacterial composition on the scar and unwounded skin was determined using 16S RNA gene-based pyrosequencing analysis, and skin around wounds was collected for RNA extraction. Compared with the control group, the overall density and composition of skin bacteria were altered, and the proportion of Staphylococcus-related sequences was reduced in the vancomycin-treated group. Moreover, vancomycin treatment decreased the expression of RegIIIγ and interleukin (IL)-17 in the wounded skin. Taken together, our data demonstrate that antibiotic treatment decreases the bacterial density and alters the bacterial composition in skin wounds, followed by a decrease in RegIIIγ expression, which may contribute to the delayed wound repair. Our findings also indicate that antibiotic therapy should be carefully considered in the treatment of skin injury.

Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs

We generated a neonatal pig model with human infant gut microbiota (HGM) to study the effect of a probiotic on the composition of the transplanted microbiota following rotavirus vaccination and challenge. All the HGM-transplanted pigs received two doses of an oral attenuated rotavirus vaccine. The gut microbiota of vaccinated pigs were investigated for effects of Lactobacillus rhamnosus GG (LGG) supplement and homotypic virulent human rotavirus (HRV) challenge. High-throughput sequencing of V4 region of 16S rRNA genes demonstrated that HGM-transplanted pigs carried microbiota similar to that of the C-section delivered baby. Firmicutes and Proteobacteria represented over 98% of total bacteria in the human donor and the recipient pigs. HRV challenge caused a phylum-level shift from Firmicutes to Proteobacteria. LGG supplement prevented the changes in microbial communities caused by HRV challenge. In particular, members of Enterococcus in LGG-supplemented pigs were kept at the baseline level, while they were enriched in HRV challenged pigs. Taken together, our results suggested that HGM pigs are valuable for testing the microbiota’s response to probiotic interventions for treating infantile HRV infection.

Human milk oligosaccharides shorten rotavirus-induced diarrhea and modulate piglet mucosal immunity and colonic microbiota

The impact of human milk oligosaccharides (HMO) on mucosal immunity, gut microbiota and response to rotavirus (RV) infection was investigated in the piglet model. Newborn piglets were fed with formula alone (FF) or formula supplemented with 4 g l(-1) HMO (HMO) or a prebiotic mixture of 9:1 short-chain galactooligosaccharides (3.6 g l(-1)) and long-chain fructooligosaccharides (0.4 g l(-1)) (PRE) (n=19-21 per group) for 15 days. Piglets (n=7-8) in each dietary group were orally infected with porcine rotavirus (RV) OSU strain on d10, and stool consistency was assessed daily. Blood, small intestine and colonic contents were collected at day 15. Serum RV-specific antibody concentrations, intestinal histomorphology, RV non-structural protein-4 (NSP4) and cytokine mRNA expression were assessed. Colonic content pH, dry matter (DM) and short-chain fatty acid concentrations were measured. Ascending colonic microbiota was analyzed by 16S rRNA gene v1-3 region pyrosequencing. HMO- and PRE-fed groups had shorter duration of diarrhea than FF piglets. Infection changed intestinal histomorphology, increased serum RV-specific antibody response and intestinal RV NSP4 expression, and modulated ileal cytokine expression. HMO enhanced T helper type 1 (interferon-gamma) and anti-inflammatory (interleukin-10) cytokines in the ileum, while prebiotics promoted RV-specific immunoglobulin M response to the infection. RV infection and HMO supplementation altered intraluminal environment and gut microbiota. HMO increased pH and lowered DM of colonic contents and enhanced the abundance of unclassified Lachnospiraceae, which contains numerous butyrate-producing bacteria. In conclusion, HMO and prebiotics did not prevent the onset of RV infection but reduced the duration of RV-induced diarrhea in piglets, in part, by modulating colonic microbiota and immune response to RV infection.

Targeting the human genome-microbiome axis for drug discovery: inspirations from global systems biology and traditional Chinese medicine

Most chronic diseases impairing current human public health involve not only the human genome but also gene-environment interactions, and in the latter case the gut microbiome is an important factor. This makes the classical single drug-receptor target drug discovery paradigm much less applicable. There is widespread and increasing international interest in understanding the properties of traditional Chinese medicines (TCMs) for their potential utilization as a source of new drugs for Western markets as emerging evidence indicates that most TCM drugs are actually targeting both the host and its symbiotic microbes. In this review, we explore the challenges of and opportunities for harmonizing Eastern-Western drug discovery paradigms by focusing on emergent functions at the whole body level of humans as superorganisms. This could lead to new drug candidate compounds for chronic diseases targeting receptors outside the currently accepted "druggable genome" and shed light on current high interest issues in Western medicine such as drug-drug and drug-diet-gut microbial interactions that will be crucial in the development and delivery of future therapeutic regimes optimized for the individual patient.

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

Despite a long-suspected role in the development of human colorectal cancer (CRC), the composition of gut microbiota in CRC patients has not been adequately described. In this study, fecal bacterial diversity in CRC patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the V3 region of the 16S ribosomal RNA gene. Both principal component analysis and UniFrac analysis showed structural segregation between the two populations. Forty-eight operational taxonomic units (OTUs) were identified by redundancy analysis as key variables significantly associated with the structural difference. One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant. Real-time quantitative PCR further validated the significant reduction of butyrate-producing bacteria in the gut microbiota of CRC patients by measuring the copy numbers of butyryl-coenzyme A CoA transferase genes (Mann-Whitney test, P<0.01). Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients.