Alpha Diversity Of Gut Microbiota Research Articles

The Role Transition of Dietary Species Richness in Modulating the Gut Microbial Assembly and Postweaning Performance of a Generalist Herbivore.

ABSTRACTWhen facing a food shortage, generalist herbivores can respond by expanding their dietary species richness (DSR) to maximize energy collection, regardless of whether forages are preferred or not. Higher DSR usually indicates higher nutrient adequacy and better health. However, the high-DSR diet containing a large proportion of preferred species or a large proportion of less-preferred species means different things to an animal. It is still unknown how different shift patterns in DSR would affect distinctly the performance of animals via altering gut microbiota. We examined the gut microbial composition, diversity, community assembly processes, and performance of a generalist herbivore, Lasiopodomys brandtii, in a feeding experiment with increased levels of simulated DSR shifting from preferred plant species to less preferred ones. We found the survival rate and body growth of Brandt’s voles showed a dome-shaped association with DSR: species performance increased initially with the increase of preferred plant species but declined with the increase of less-preferred food items. Several microbial taxa and functions closely related to the metabolism of amino acids and short-chain fatty acids also showed a dome-shaped association with DSR, which is consistent with the observation of performance change. However, the alpha diversities of gut microbiota increased linearly with DSR. The null model and phylogenetic analysis suggested that stochastic processes dominate at low DSR diets, whereas deterministic processes prevail at high DSR diets. These results suggest that the role of DSR in regulating animal performance by gut microbiota depends on the number of preferred forage items.IMPORTANCE The plant species diversity varies greatly under the influence of both climate change and human disturbance, which may negatively affect the productivity as well as the variability of organisms (e.g., small herbivores) at the next trophic level. It is still unknown how gut microbiota of small herbivores respond to such changes in dietary species richness. Our manipulative food experiment revealed that dietary species richness can affect the composition, functions, and community assembly of gut microbiota of Brandt’s vole in a nonlinear way. Given the fast-growing interest in therapeutic diets to treat dysbiosis and to improve health conditions, our study highlights the need to consider not just the variety of consumed food but also the principles of rational nutrition.

Dysbiosis of Gut Microbiota in Patients with Post-Stroke Cognitive Impairment

To identify the differences in the composition of gut microbiota of patients with post-stroke cognitive impairment (PSCI) in comparison with the normal cognition healthy controls (HC), and to study the potential association between gut microbiota and cognition function. A total of 24 patients were recruited for the PSCI group, which was matched with 23 healthy subjects with no history of cardiovascular disease recruited over the same period for the control group. Fecal samples were collected for both groups, and Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) were used to evaluate cognitive functions. The abundance, diversity and group difference of gut bacterial communities were determined with 16S rRNA gene sequencing, and the correlations between differences in bacterial species of the gut microbiota and cognitive function scores were examined with redundancy analysis (RDA)/canonical correspondence analysis (CCA). There was no significant difference in the general data or the alpha diversity of gut microbiota between the two groups ( P>0.05). Inter-group comparison of microbial species composition revealed differences at the phylum and species levels, mainly represented as reduction in the relative abundance of Firmicutes and Bacteroidetes, and the relative enrichment of Proteobacteria. The relative abundance of Intestinibacter bartlettii, uncultured bacterium Tyzzerella_3, Lactobacillus gasseri, and Fusicatenibacter saccharivorans of phylum Firmicutes in the PSCI patients were significantly reduced in comparison to that of the HC (LDA score>2), and these bacteria were positively correlated with MMSE and MoCA scores. In addition, the Ruminococcus gnavus and Faecalimonas umbilicata of phylum Firmicutes and uncultured bacterium Prevotellaceae_NK3 B31 group of phylum Bacteroidetes were significantly enriched in comparison with those of the HC (LDA score>2), and these bacteria were negatively correlated with MMSE and MoCA scores. There were also correlations among these bacteria. In this study, we observed compositional differences between the gut microbiota of PSCI patients and those of HC, and revealed that the differences were correlated, to some degree, to the cognitive functions, which will provide new perspectives for the clinical diagnosis and treatment of PSCI.

Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development

The environmental stresses could significantly affect the structure and functions of microbial communities colonized in the gut ecosystem. However, little is known about how engineered nanoparticles (ENPs), which have recently become a common pollutant in the environment, affect the gut microbiota across fish development. Based on the high-throughput sequencing of the 16S rRNA gene amplicon, we explored the ecological succession of gut microbiota in zebrafish exposed to nanoparticles for three months. The nanoparticles used herein including titanium dioxide nanoparticles (nTiO2, 100 μg/L), zinc oxide nanoparticles (nZnO, 100 μg/L), and selenium nanoparticles (nSe, 100 μg/L). Our results showed that nanoparticles exposure reduced the alpha diversity of gut microbiota at 73–90 days post-hatching (dph), but showed no significant effects at 14–36 dph. Moreover, nTiO2 significantly (p < 0.05) altered the composition of the gut microbial communities at 73–90 dph (e.g., decreasing abundance of Cetobacterium and Vibrio). Moreover, we found that homogeneous selection was the major process (16.6–57.8%) governing the community succession of gut microbiota. Also, nanoparticles exposure caused topological alterations to microbial networks and led to increased positive interactions to destabilize the gut microbial community. This study reveals the environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development, which provides novel insights to understand the gut microbial responses to ENPs over the development of aquatic animals.

Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus.

Hibernation represents a state of fasting because hibernators cease eating in the torpid periods. Therefore, food deprivation during hibernation is expected to modify the gut microbiota of host. However, there are few reports of gut microbiota in food-storing hibernators that feed during the interbout arousals. Here we collected fecal samples of Siberian chipmunk T. sibiricus to character and examine changes in the gut microbiota at various stages relative to hibernation: pre-hibernation, early-hibernation, mid-hibernation, late-hibernation, and post-hibernation. Compared to the pre-hibernation state, alpha-diversity of gut microbiota was significantly increased during the interbout arousal periods. In addition, beta-diversity of the fecal communities from pre-hibernation and interbout arousal periods grouped together, and post-hibernation gut microbiota resembled the counterpart at late-hibernation. Hibernation significantly decreased the relative abundance of Firmicutes but increased Bacteroidetes, reflecting a shift of microbiota toward taxa in favor of host-derived substrates. The increased abundance of Ruminococcaceae_UCG-014, Lactobacillus, and Christensenellaceae_R-7_group in gut microbiota may help the chipmunks reduce intestinal inflammation and then maintain healthy bowel during hibernation. KEGG pathway indicated that hibernation altered the metabolic function of gut microflora of T. sibiricus.Our study provides evidence that the gut microbiota of food-storing hibernators, despite feeding during the interbout arousals, shows similar response to hibernation that has well documented in fat-storing counterparts, suggesting the potential for a core gut microbiota during hibernation of mammals. Importantly, these results will broaden our understanding of the effects of hibernation on gut microbiota of mammal hibernators.

Protein Intake, Metabolic Status and the Gut Microbiota in Different Ethnicities: Results from Two Independent Cohorts.

Background: Protein intake has been associated with the development of pre-diabetes (pre-T2D) and type 2 diabetes (T2D). The gut microbiota has the capacity to produce harmful metabolites derived from dietary protein. Furthermore, both the gut microbiota composition and metabolic status (e.g., insulin resistance) can be modulated by diet and ethnicity. However, to date most studies have predominantly focused on carbohydrate and fiber intake with regards to metabolic status and gut microbiota composition. Objectives: To determine the associations between dietary protein intake, gut microbiota composition, and metabolic status in different ethnicities. Methods: Separate cross-sectional analysis of two European cohorts (MetaCardis, n = 1759; HELIUS, n = 1528) including controls, patients with pre-T2D, and patients with T2D of Caucasian/non-Caucasian origin with nutritional data obtained from Food Frequency Questionnaires and gut microbiota composition. Results: In both cohorts, animal (but not plant) protein intake was associated with pre-T2D status and T2D status after adjustment for confounders. There was no significant association between protein intake (total, animal, or plant) with either gut microbiota alpha diversity or beta diversity, regardless of ethnicity. At the species level, we identified taxonomical signatures associated with animal protein intake that overlapped in both cohorts with different abundances according to metabolic status and ethnicity. Conclusions: Animal protein intake is associated with pre-T2D and T2D status but not with gut microbiota beta or alpha diversity, regardless of ethnicity. Gut microbial taxonomical signatures were identified, which could function as potential modulators in the association between dietary protein intake and metabolic status.

Composition of the microbial communities at different body sites in women with preterm birth and their newborns

ObjectiveIn this study, we aimed to examine the changes in the composition of vaginal and gut microbiota during the third trimester of pregnancy among women who delivered preterm. To further understand the relationship of these changes to preterm birth, we analyzed the microecology of vaginal and gut microbiota in mothers, as well as oral and gut microbiota in their newborns, and then compared the microecological characteristics of the microbiome at different body sites between the mothers and their newborns, as well as between the mothers and between the newborns from different groups. MethodsIn total, 26 women who delivered at Zhujiang Hospital, Southern Medical University (China) from July 2020 to January 2021 were categorized into the preterm and term groups. A blank swab and laboratory air and water samples were collected as part of the control group. We collected maternal vaginal and rectal samples, as well as neonatal oral and rectal samples. Total DNA from different parts of the swabs was extracted and sequenced using the 16s rRNA technique. Then, the data was analyzed using bioinformatics and statistical analysis. ResultsThe abundance and alpha diversity of vaginal microbiota in the preterm group was found to be higher, but the difference was not statistically significant. There were significant differences in beta diversity of vaginal microbiota between the two groups (p ​< ​0.05). The levels of Rothia and Gemella in the gut microbiota of women who had delivered preterm were significantly lower (p ​< ​0.05). The alpha diversity of gut microbiota and neonatal oral and gut microbiota in women who had delivered preterm was lower. No significant differences were observed in alpha and beta diversity between the two groups in maternal gut microbiota and neonatal oral and gut microbiota. In the newborns in both groups, some species of oral microbiota were consistent with their mother's vaginal microbiota, and some species of gut microbiota in the newborns in both groups were consistent with their mother's gut microbiota. ConclusionsVaginal and gut microbiota in women who had given birth preterm were noticeably different from the vaginal and gut microbiota of women who had delivered at term, and it was probably related to preterm birth. Oral and gut microbiotas of preterm newborns were also noted to be different from that of the term newborns. It suggests that the changes in the microbiome of the newborns could be related to preterm birth. Some part of the newborns’ microbiota probably originates in the uterus.

Lycium barbarum polysaccharide attenuates emotional injury of offspring elicited by prenatal chronic stress in rats via regulation of gut microbiota

Stress during pregnancy is not only detrimental to a woman's own physical and mental health, but can also cause changes in the intrauterine environment and even have an impact on later growth and development, this study was designed to understand the changes of gut microbiota in the maternal and offspring caused by prenatal chronic stress, and to explore the regulatory effect of LBP on gut microbiota, and then to improve the emotional damage caused by prenatal chronic stress in the offspring. A rat model of prenatal chronic stress was made and used LBP to intervene by gavage. Fresh feces of offspring were collected, the concentration of microbial metabolites were tested by ELISA. Illumina MiSeqPE300 sequencing technology was used to determine the sequence of 16S rRNA V3-V4 of microorganisms. On the PND 42, the emotional function of offspring were tested by open-field test (OFT), sucrose preference test (SPT) and tail of suspend test (TST). Results indicated that stress factors increased the plasma corticosterone level of rats during pregnancy and they appeared depressive behaviors. The body weight of offspring during prenatal chronic stress was lower than the control group, and the plasma corticosterone level was increased. Prenatal chronic stress had a significant impact on emotional performance of the offspring on OFT, SPT and TST. Alpha diversity of gut microbiota and microbiota composition in offspring of prenatal chronic stress was attenuated and some relationships existed between these parameters. LBP treatment reduced offspring’s plasma corticosterone level and improved their body weight, changed the emotional function, increased the diversity of gut microbiota. Collectively, these findings disclose that prenatal chronic stress not only causes emotional injury on the offspring, but also changes the gut microbiota of the mother and offspring; LBP may regulate the intestinal flora of the mother, then reducing the influence of stress factors on the emotional injury of offspring.

Spontaneous preterm delivery is reflected in both early neonatal and maternal gut microbiota

BackgroundAberrant gut microbiota composition in preterm neonates is linked to adverse health consequences. Little is known about the impact of perinatal factors or maternal gut microbiota on initial preterm gut colonization.MethodsFecal samples were collected from 55 preterm neonates (<35 gestational weeks), 51 mothers, and 25 full-term neonates during the first 3–4 postpartum days. Gut microbiota composition was assessed using 16S ribosomal RNA gene sequencing.ResultsPreterm neonates exhibited significantly lower gut microbiota alpha diversity and distinct beta diversity clustering compared to term neonates. Spontaneous preterm birth was associated with distinct initial gut microbiota beta diversity as compared to iatrogenic delivery. Gestational age or delivery mode had no impact on the preterm gut microbiota composition. The cause of preterm delivery was also reflected in the maternal gut microbiota composition. The contribution of maternal gut microbiota to initial preterm gut colonization was more pronounced after spontaneous delivery than iatrogenic delivery and not dependent on delivery mode.ConclusionsThe initial preterm gut microbiota is distinct from term microbiota. Spontaneous preterm birth is reflected in the early neonatal and maternal gut microbiota. Transmission of gut microbes from mother to neonate is determined by spontaneous preterm delivery, but not by mode of birth.ImpactThe initial gut microbiota in preterm neonates is distinct from those born full term. Spontaneous preterm birth is associated with changes in the gut microbiota composition of both preterm neonates and their mothers. The contribution of the maternal gut microbiota to initial neonatal gut colonization was more pronounced after spontaneous preterm delivery as compared to iatrogenic preterm delivery and not dependent on delivery mode.Our study provides new evidence regarding the early gut colonization patterns in preterm infants.Altered preterm gut microbiota has been linked to adverse health consequences and may provide a target for early intervention.

Commensal microbiota contributes to predicting the response to immune checkpoint inhibitors in non-small-cell lung cancer patients.

Immunotherapy against cancer, through immune checkpoint inhibitors targeting the programmed cell death‐1/programmed cell death‐ligand 1 axis, is particularly successful in tumors by relieving the immune escape. However, interindividual responses to immunotherapy are often heterogeneous. Therefore, it is essential to screen out predictive tumor biomarkers. In this study, we analyzed the commensal microbiota in stool samples and paired sputum samples from 75 metastatic non‐small‐cell lung cancer (NSCLC) patients at baseline and during treatment with immune checkpoint inhibitors. Results showed distinct microbes’ signatures between the gut microbiota and paired respiratory microbiota. The alpha diversity between the gut and respiratory microbiota was uncorrelated, and only the gut microbiota alpha diversity was associated with anti‐programmed cell death‐1 response. Higher gut microbiota alpha diversity indicated better response and more prolonged progression‐free survival. Comparison of bacterial communities between responders and nonresponders showed some favorable/unfavorable microbes enriched in responders/nonresponders, indicating that commensal microbiota had potential predictive value for the response to immune checkpoint inhibitors. Generally, some rare low abundance gut microbes and high abundance respiratory microbes lead to discrepancies in microbial composition between responders and nonresponders. A significant positive correlation was observed between the abundance of Streptococcus and CD8+ T cells. These results highlighted the intimate relationship between commensal microbiota and the response to immunotherapy in NSCLC patients. Gut microbiota and respiratory microbiota are promising biomarkers to screen suitable candidates who are likely to benefit from immune checkpoint inhibitor‐based immunotherapy.

Understanding the effects of intramuscular injection and feed withdrawal on Salmonella Typhimurium shedding and gut microbiota in pullets

BackgroundGut microbiota plays a key role in health, immunity, digestion, and production in layers. Factors such as environment, diet, diseases, stress, and flock management significantly affect gut microbiota; however, it is not known how potential stressors such as intramuscular injections or feed withdrawal alter the composition of gut microbiota that result in increased the shedding level of foodborne pathogens. In the current study, the effects of intramuscular corticosterone injection and feed withdrawal were evaluated to understand their role in Salmonella Typhimurium shedding and changes in the composition of gut microbiota in layers.ResultsSalmonella shedding was observed for 8 weeks post-infection. There was a significant increase in Salmonella Typhimurium count after intramuscular injection and feed withdrawal. The Salmonella infected and the negative control groups showed significant differences in the abundance of different genera in gut microbiota at week 1 and up to week 7 post infection. The infected group showed a significant reduction in alpha diversity of gut microbiota. Firmicutes reduced significantly (P < 0.05) after intramuscular injection, while the feed withdrawal groups did not cause any significant changes in Proteobacteria-Firmicutes ratio. Furthermore, intramuscular injection resulted in a significant change in alpha diversity of gut microbiota.ConclusionsExposure of chicks to relatively low dose of Salmonella Typhimurium can lead to persistent shedding in pullets. The Salmonella Typhimurium infection disrupted the gut microbiota composition immediately after infection. The potential stress of intramuscular injection and feed withdrawal significantly increased the Salmonella Typhimurium count in faeces. The intramuscular injection also resulted in a significant alteration of the Proteobacteria-Firmicutes ratio, which could increase the risk of dysbiosis.

Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age

BackgroundColonization of intestinal microbiota in ruminant during the early life is important to host health, metabolism and immunity. Accumulating evidence revealed the ameliorative effect of milk replacer administration in the gut microbial development of early-weaned ruminants. Yimeng black goats (YBGs) inhabiting Shandong, China show a complex intestinal microbial ecosystem, but studies of their gut microbiota are still insufficient to report. Here, this study was performed to investigate how the gut microbiota develops in weaned YBGs with the effect of age and milk replacer.ResultsResults indicated that both age and milk replacer were important factors to change the gut microbiota of YBGs. Although the alpha diversity of gut microbiota did not change with the age of YBGs, the taxonomic compositions significantly changed. The relative abundance of some beneficial bacteria such as Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Eubacterium and Barnesiella significantly decreased and subsequently increase with age, which contributes to maintain the stability of intestinal environment and realize the diversity of intestinal functions. The relative abundance of Porphyromonas, Brevundimonas, Flavobacterium, Stenotrophomonas, Propionibacterium, Acinetobacter, Enterococcus and Clostridium belong to pathogenic bacteria in milk replacer-treated YBGs was significantly decreased. Additionally, some beneficial bacteria such as Ruminococcus, Ruminococcaceae, Christensenellaceae and Ruminiclostridium also display a trend of decreasing first followed by gradually increasing.ConclusionsThis study first revealed the gut bacterial community alterations in YBGs with the effect of age and milk replacer. This study also characterized the gut microbial distribution in YBGs with different ages and provided better insight into microbial population structure and diversity of YBGs. Moreover, milk replacer may serve as a good applicant for improving gut microbial development in early-weaned YBGs.

Cecal microbiota contribute to the development of woody breast myopathy

The objective of this study was to characterize the bacterial diversity of cecal microbiota in broilers related to breast phenotype, diet, and genetic strain. Broilers from 2 genetic strains (120 birds/strain) were fed a control diet (15 birds/pen) and an amino acid reduced diet (15 birds/pen, digestible lysine, total sulfur amino acids, and threonine reduced by 20% compared to the control diet). At 8 wk of age, 4 male broilers with normal breast (NB, 1 chick per pen) and 4 male broilers with woody breast (WB, 1 chick per pen) were selected for each treatment (strain × diet). The DNA of cecal samples was extracted and the 16S rRNA genes were sequenced and analyzed. There were no differences (P > 0.05) in the alpha diversity of gut microbiota between 2 phenotypes (NB vs. WB), 2 strains, or 2 diets (control vs. reduced). However, principal coordinate analysis plots (beta diversity) revealed that there were composition differences in samples between the 2 phenotypes (P = 0.001) and the 2 diets (P = 0.024). The most abundant phyla in all samples were Firmicutes, followed by Bacteroidetes and Proteobacteria. There were differences (false discovery rate, FDR < 0.05) in bacterial relative abundance between phenotypes and between diet treatments, but not (FDR > 0.05) between the 2 genetic strains. Selenomonas bovis (12.6%) and Bacteroides plebeius (12.3%) were the top 2 predominant bacteria in the ceca of WB birds; however, the relative abundances of these 2 bacteria were only 5.1% and 1.2% in NB birds, respectively. Function analysis predicted that the metabolic activities differed (q < 0.05) only between phenotypes. The microbiota of WB birds was characterized as reduced glycolysis and urea cycle but increased tricarboxylic acid (TCA) cycles, sugar degradation, and purine and pyrimidine nucleotides biosynthesis. Further studies are needed to investigate if WB incidence could be reduced by regulating gut microbiota and the potential mechanism that leads to decreased WB incidence.

Diet, Immunity, and Microbiota Interactions: An Integrative Analysis of the Intestine Transcriptional Response and Microbiota Modulation in Gilthead Seabream (Sparus aurata) Fed an Essential Oils-Based Functional Diet.

Essential oils (EOs) are promising alternatives to chemotherapeutics in animal production due to their immunostimulant, antimicrobial, and antioxidant properties, without associated environmental or hazardous side effects. In the present study, the modulation of the transcriptional immune response (microarray analysis) and microbiota [16S Ribosomal RNA (rRNA) sequencing] in the intestine of the euryhaline fish gilthead seabream (Sparus aurata) fed a dietary supplementation of garlic, carvacrol, and thymol EOs was evaluated. The transcriptomic functional analysis showed the regulation of genes related to processes of proteolysis and inflammatory modulation, immunity, transport and secretion, response to cyclic compounds, symbiosis, and RNA metabolism in fish fed the EOs-supplemented diet. Particularly, the activation of leukocytes, such as acidophilic granulocytes, was suggested to be the primary actors of the innate immune response promoted by the tested functional feed additive in the gut. Fish growth performance and gut microbiota alpha diversity indices were not affected, while dietary EOs promoted alterations in bacterial abundances in terms of phylum, class, and genus. Subtle, but significant alterations in microbiota composition, such as the decrease in Bacteroidia and Clostridia classes, were suggested to participate in the modulation of the intestine transcriptional immune profile observed in fish fed the EOs diet. Moreover, regarding microbiota functionality, increased bacterial sequences associated with glutathione and lipid metabolisms, among others, detected in fish fed the EOs supported the metabolic alterations suggested to potentially affect the observed immune-related transcriptional response. The overall results indicated that the tested dietary EOs may promote intestinal local immunity through the impact of the EOs on the host-microbial co-metabolism and consequent regulation of significant biological processes, evidencing the crosstalk between gut and microbiota in the inflammatory regulation upon administration of immunostimulant feed additives.

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

BackgroundGastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls.ResultsWe found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients.ConclusionsOur analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.

Effect of Antibiotics on The Gut Microbiota in Children with Chronic Pancreatitis

Objectives: Little is known about the effect of antibiotic treatment on the gut microbiota in children with chronic pancreatitis (CCP). Our objective was to identify the effect of antibiotic treatment on the gut microbiota in children with chronic pancreatitis (CCP), the main gut microbiota genera and characterize the patients’ functional mutations after using antibiotics. Methods: The 16S rRNA sequencing method was used to compare the gut microbiota of healthy controls (HCs) with CCP using and not using antibiotics. Results: All CCP demonstrated a significantly reduced alpha diversity of the gut microbiota (P＜0.01). The gut microbiota's alpha diversity and the abundance of genera’s beta diversity did not show statistical differences between the non-antibiotics and antibiotics groups. There were 15 altered genera with common abundance in the non-antibiotics and antibiotics groups compared to the HC group. The area under the curve (AUC) of the top three probiotics, i.e., Faecalibacterium, Eubacterium, and Subdoligranulum, was 0.91. Among the 13 genera altered in the non-antibiotics group, the top three genera were not appropriate as biomarkers for cases receiving antibiotics. Compared to these 13 genera, the differences between the genera and the proportion of gram-positive bacteria in the 17 genera altered only in the antibiotics group were not statistically significant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the antibiotics caused alterations in the abundance of certain genera. The enriched functions and the altered gut microbiota in the two groups had their enriched functions. Conclusion: The use of antibiotics affects the gut microbiota of CCP, but the effect of disease on gut microbiota is still obvious, which may help diagnosis and further investigation into the pathogenic mechanisms of CP. Chronic pancreatitis (CP) is a persistent fibro-inflammatory process of the pancreas associated with genetic, environmental, and other pathogenic factors. This disease eventually led to the pancreas' irreversible injury and increased risk of pancreatic cancer and impaired mental health [1-3].

Inbreeding Alters the Gut Microbiota of the Banna Minipig.

Simple SummaryThe mammalian gut microbiota is an indispensable part of host health. The gut microbiota plays a crucial role in nutrient digestibility, preventing colonization of pathogens and maintaining the host immune system. Host genetics has been conclusively shown to closely related to gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity, however, remarkably little is understood about the gut microbiota of pigs during inbreeding. The Banna minipig inbred is the world’s first successful large mammalian experimental animal inbred line since 1980 from full and half-siblings of the Diannan small-ear pig. Now, Banna minipig inbred has been inbred for over 37 generations, and the inbreeding coefficient is more than 99%. This study is the first to characterize and compare the composition and function of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to better understand the influence of inbreeding on the gut microbiota.The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner.

T cell immunoglobulin and mucin domain-containing protein-3 (Tim-3) is an immune checkpoint molecule and a target for anti-cancer therapy. In this study, we examined whether gut microbiota manipulation altered the anti-tumour efficacy of Tim-3 blockade. The gut microbiota of mice was manipulated through the administration of antibiotics and oral gavage of bacteria. Alterations in the gut microbiome were analysed by 16S rRNA gene sequencing. Gut dysbiosis triggered by antibiotics attenuated the anti-tumour efficacy of Tim-3 blockade in both C57BL/6 and BALB/c mice. Anti-tumour efficacy was restored following oral gavage of faecal bacteria even as antibiotic administration continued. In the case of oral gavage of Enterococcus hirae or Lactobacillus johnsonii, transferred bacterial species and host mouse strain were critical determinants of the anti-tumour efficacy of Tim-3 blockade. Bacterial gavage did not increase the alpha diversity of gut microbiota in antibiotic-treated mice but did alter the microbiome composition, which was associated with the restoration of the anti-tumour efficacy of Tim-3 blockade. Conclusively, our results indicate that gut microbiota modulation may improve the therapeutic efficacy of Tim-3 blockade during concomitant antibiotic treatment. The administered bacterial species and host factors should be considered in order to achieve therapeutically beneficial modulation of the microbiota.

Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi

BackgroundGut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of vertebrate, remains less explored. In this study, we characterized the gut microbial communities of urochordate ascidian (Halocynthia roretzi) across the changes of season and starvation stress using a comprehensive set of omic approaches including 16S rRNA gene amplicon sequencing, shotgun metagenomics, metabolomic profiling, and transcriptome sequencing.ResultsThe 16S rRNA gene amplicon profiling revealed that ascidians harbor indigenous gut microbiota distinctly different to the marine microbial community and significant variations in composition and abundance of gut bacteria, with predominant bacterial orders representing each season. Depressed alpha-diversities of gut microbiota were observed across starvation stress when compared to the communities in aquafarm condition. Synechococcales involving photosynthesis and its related biosynthesis was reduced in abundance while the enrichments of Xanthomonadales and Legionellales may facilitate bile acid biosynthesis during starvation. Metabolomics analysis found that long chain fatty acids, linolenic acid, cyanoamino acid, and pigments derived from gut bacteria were upregulated, suggesting a beneficial contribution of the gut microbiome to the ascidian under starvation stress.ConclusionsOur findings revealed seasonal variation of ascidian gut microbiota. Defense and energy-associated metabolites derived from gut microbiome may provide an adaptive interplay between gut microbiome and ascidian host that maintains a beneficial metabolic system across season and starvation stress. The diversity-generating metabolisms from both microbiota and host might lead to the co-evolution and environmental adaptation.Graphical

Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger.

It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.

Micro-encapsulated essential oils and organic acids combination improves intestinal barrier function, inflammatory responses and microbiota of weaned piglets challenged with enterotoxigenic Escherichia coli F4 (K88+).

This study evaluated the effects of micro-encapsulated (protected) organic acids (OA) and essential oils (EO) combination, P(OA + EO), and effects of a regular blend of free acids (FA) on the growth, immune responses, intestinal barrier and microbiota of weaned piglets challenged with enterotoxigenic Escherichia coli (ETEC) F4 (K88+). A total of 30 crossbred (Duroc × Landrace × Large White) weaned barrows (7.41 ± 0.06 kg, 28 d old) were assigned randomly to 5 treatments: 1) non-challenged positive control (PC), 2) ETEC F4 (K88+)-challenged negative control (NC), 3) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + free acidifier (FA) at 5 g/kg, 4) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + P(OA + EO) at 1 g/kg (P1), 5) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + P(OA + EO) at 2 g/kg (P2). Each dietary treatment had 6 replicates of one piglet each and the study lasted for 3 wk. On d 7, pigs in NC, FA, P1 and P2 were orally dosed with 10 mL of ETEC F4 (K88+) culture (1 × 109 CFU/mL). From d 7 to 14 after the ETEC F4 (K88+) challenge, P1 increased gain-to-feed ratio (G:F) significantly (P < 0.05) compared with NC and FA groups. From d 14 to 21, P2 increased the average daily gain of pigs (P < 0.05) compared with NC and FA groups. Compared with NC, P2 reduced tumor necrosis factor-α (TNF-α), interleukin (IL)-6 and IL-10 concentrations (P < 0.05) in sera collected at 4 h later after ETEC F4 (K88+) challenge. On d 21, P1 increased occludin and zonula occludens-1 protein expression in ileum compared with NC (P < 0.05). After this 3-wk experiment, alpha diversity of gut microbiota was decreased by P2 compared with PC, and P1 increased the relative abundance of Lactobacillus in ileum, cecum and colon (P < 0.05). In conclusion, dietary P(OA + EO) additive at 2 g/kg combined with antibiotics could improve piglet performance and attenuate inflammation, and P(OA + EO) additive at 1 g/kg combined with antibiotics improved intestinal barrier and increased beneficial microbiota composition after an F4 (K88+) challenge.