Changes In Fecal Microbiota Research Articles

Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease

Exclusive enteral nutrition (EEN) is a first-line therapy for pediatric Crohn's disease (CD), but protective mechanisms remain unknown. We established a prospective pediatric cohort to characterize the function of fecal microbiota and metabolite changes of treatment-naive CD patients in response to EEN (German Clinical Trials DRKS00013306). Integrated multi-omics analysis identified network clusters from individually variable microbiome profiles, with Lachnospiraceae and medium-chain fatty acids as protective features. Bioorthogonal non-canonical amino acid tagging selectively identified bacterial species in response to medium-chain fatty acids. Metagenomic analysis identified high strain-level dynamics in response to EEN. Functional changes in diet-exposed fecal microbiota were further validated using gut chemostat cultures and microbiota transfer into germ-free Il10-deficient mice. Dietary model conditions induced individual patient-specific strain signatures to prevent or cause inflammatory bowel disease (IBD)-like inflammation in gnotobiotic mice. Hence, we provide evidence that EEN therapy operates through explicit functional changes of temporally and individually variable microbiome profiles.

Dietary nucleotides drive changes in infant fecal microbiota in vitro and gut microbiota-gut-brain development in neonatal rats: A potential “nitrogen source” for early microbiota growth

Various dietary factors in human milk are important nutrients for the formation of the infant gut microbiota (GM). While promoting the growth of the GM, some human milk components that are difficult to absorb and utilize will be broken down by the GM, and converted into nutrients that the baby can use, such as breast milk oligosaccharides—the ‘carbon source’ for infant GM. This study reveals that nucleotides (NTs), significant non-protein nitrogen sources in human milk, can enhance the abundance of beneficial microbial genera such as g_Bifidobacterium, g_Bacteroides, and g_Blautia in in vitro fecal fermentation fluids of infants at low doses (2 mg/mL). Conversely, high doses of NTs (20 mg/mL) increased the abundance of g_Escherichia-Shigella. Furthermore, low-dose NTs fermentation broth significantly enhanced the expression of neurodevelopmental marker genes such as Tuj1, Sox2, Dcx, and NeuN in NE-4C neural stem cells, whereas a single NTs digestion broth did not exhibit significant activity. However, in vivo studies using neonatal rats as a model demonstrated that both low-dose NTs fermentation broth and NTs digestive juices promoted behavioral development in neonatal rats (PND 20) and neuron maturation in the prefrontal cortex and hippocampus. Non-targeted metabolomics results indicate that low-dose dietary NTs promote the production of certain neuroregulatory metabolites in infant fecal fermentation, such as uridine, L-tyrosine, L-glutamic acid, and succinic acid. These findings suggest that NTs may serve as an important “nitrogen source” during GM formation in early life and have a dose effect in driving the development of the microbiota-gut-brain axis in early life.

Changes in faecal microbiota in 6‐ to 12‐year‐old children after a new nutritional strategy: the ALINFA randomised controlled trial

SummaryGut microbiota seems to play a critical role in health and disease. This study aimed to evaluate the effect of a nutritional intervention in children 6–12 years old on the microbiota and to identify possible dietary components involved in the change. A 2‐month parallel, controlled randomised trial was conducted. The nutritional intervention was based on the recommendations of the Mediterranean diet, for both intervention groups, with the difference that in the ALINFA group a more intensive intervention based on a complete diet, while in the control group, dietary advice was provided. After the intervention, ALINFA group showed an increase in the richness and diversity of their microbiota as well as changes in the abundance of different bacterial heels. These changes were mainly influences by fibre intake and the type of fat consumed. The ALINFA nutritional intervention seems to be able to positively influence children's microbiota, showing significant changes within 2 months.

Icaritin-curcumol activates CD8+ T cells through regulation of gut microbiota and the DNMT1/IGFBP2 axis to suppress the development of prostate cancer

BackgroundProstate cancer (PCa) incidence and mortality rates are rising. Our previous research has shown that the combination of icariin (ICA) and curcumol (CUR) induced autophagy and ferroptosis in PCa cells, and altered lipid metabolism. We aimed to further explore the effects of the combination of ICA and CUR on gut microbiota, metabolism, and immunity in PCa.MethodsA mouse subcutaneous RM-1 cell tumor model was established. 16 S rRNA sequencing was performed to detect changes in fecal gut microbiota. SCFAs in mouse feces, and the effect of ICA-CUR on T-cell immunity, IGFBP2, and DNMT1 were examined. Fecal microbiota transplantation (FMT) was conducted to explore the mechanism of ICA-CUR. Si-IGFBP2 and si/oe-DNMT1 were transfected into RM-1 and DU145 cells, and the cells were treated with ICA-CUR to investigate the mechanism of ICA-CUR on PCa development.ResultsAfter treatment with ICA-CUR, there was a decrease in tumor volume and weight, accompanied by changes in gut microbiota. ICA-CUR affected SCFAs and DNMT1/IGFBP2/EGFR/STAT3/PD-L1 pathway. ICA-CUR increased the positive rates of CD3+CD8+IFN-γ, CD3+CD8+Ki67 cells, and the levels of IFN-γ and IFN-α in the serum. After FMT (with donors from the ICA-CUR group), tumor volume and weight were decreased. SCFAs promote tumor development and the expression of IGFBP2. In vitro, DNMT1/IGFBP2 promotes cell migration and proliferation. ICA-CUR inhibits the expression of DNMT1/IGFBP2.ConclusionsICA-CUR mediates the interaction between gut microbiota and the DNMT1/IGFBP2 axis to inhibit the progression of PCa by regulating immune response and metabolism, suggesting a potential therapeutic strategy for PCa.

Inflammatory Bowel Diseases and Non-Alcoholic Fatty Liver Disease: Piecing a Complex Puzzle Together.

Inflammatory bowel diseases (IBD), comprising Crohn's disease and ulcerative colitis, are systemic and multifaceted disorders which affect other organs in addition to the gastrointestinal tract in up to 50% of cases. Extraintestinal manifestations may present before or after IBD diagnosis and negatively impact the intestinal disease course and patients' quality of life, often requiring additional diagnostic evaluations or specific treatments. Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. Current evidence shows an increased prevalence of NAFLD (and its more advanced stages, such as liver fibrosis and steatohepatitis) in IBD patients compared to the general population. Many different IBD-specific etiopathogenetic mechanisms have been hypothesized, including chronic inflammation, malabsorption, previous surgical interventions, changes in fecal microbiota, and drugs. However, the pathophysiological link between these two diseases is still poorly understood. In this review, we aim to provide a comprehensive overview of the potential mechanisms which have been investigated so far and highlight open issues still to be addressed for future studies.

Changes in fecal microbiota during estrous cycle in healthy thoroughbred mares

Gut microbiota plays a crucial role in various physiological processes, including the regulation of the reproductive system and steroid sex hormones. Throughout the normal estrous cycle of healthy mares, the levels of estradiol-17β (E2) and progesterone (P4) in the blood exhibit periodic changes. To investigate the relationship between cyclic changes in steroid sex hormones and the gut microbiome of mares, we analyzed the fecal microbiota composition in healthy mares during the typical estrous cycle. Blood and fecal samples from five healthy mares were collected, E2 and P4 levels in serum were analyzed using radioimmunoassay (RIA), and the gut microbiome was analyzed by 16S rRNA sequencing. The overall richness and composition of the gut microbiota remained relatively stable during the normal estrous cycle in mares. The Linear Discriminant Analysis Effect Size analysis of the microbial composition during the follicular and luteal phases identified the Rhodococcus genus as differentially abundant. These findings indicate that the mare's gut microbiota's significant composition remains consistent throughout the estrous cycle. At the same time, specific low-abundance pathogenic bacteria exhibit changes that align with sexual hormonal fluctuations.

Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.

The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.

HIV-associated gut microbial alterations are dependent on host and geographic context

HIV-associated changes in intestinal microbiota are believed to be important drivers of disease progression. However, the majority of studies have focused on populations in high-income countries rather than in developing regions where HIV burden is greatest. To better understand the impact of HIV on fecal microbiota globally, we compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana. We identify significant bacterial taxa alterations with both treated and untreated HIV infection with a high degree of uniqueness in each cohort. HIV-associated taxa alterations are also significantly different between populations that report men who have sex with men (MSM) behavior and non-MSM populations. Additionally, while we find that HIV infection is consistently associated with higher soluble markers of immune activation, most specific bacterial taxa associated with these markers in each region are not shared and none are shared across all three geographic locations in our study. Our findings demonstrate that HIV-associated changes in fecal microbiota are overall distinct among geographical locations and sexual behavior groups, although a small number of taxa shared between pairs of geographic locations warrant further investigation, highlighting the importance of considering host context to fully assess the impact of the gut microbiome on human health and disease.

Changes in the fecal microbiota of breast cancer patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis.

Breast cancer (BC) is a devastating disease for women. Microbial influences may be involved in the development and progression of breast cancer. This study aimed to investigate the difference in intestinal flora abundance between breast cancer patients and healthy controls (HC) based on previous 16S ribosomal RNA (rRNA) gene sequencing results, which have been scattered and inconsistent in previous studies. In agreement with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we searched for pertinent literature in Pubmed, Embase, Cochrane Library, and Web of Science databases from build until February 1, 2023. Relative abundance, diversity of intestinal microflora by level, microbial composition, community structure, diversity index, and other related data were extracted. We used a fixed or random effects model for data analysis. We also conducted funnel plot analysis, sensitivity analysis, Egger's, and Begg's tests to assess the bias risk. A total of ten studies involving 734 BC patients were enrolled. It was pointed out that there were significant differences in the Chao index between BC and HC in these studies [SMD = - 175.44 (95% CI - 246.50 to - 104.39)]. The relative abundance of Prevotellaceae [SMD = - 0.27 (95% CI - 0.39 to - 0.15)] and Bacteroides [SMD = 0.36 (95% CI 0.23-0.49)] was significantly different. In the included articles, the relative abundance of Prevotellaceae, Ruminococcus, Roseburia inulinivorans, and Faecalibacterium prausnitzii decreased in BC. Accordingly, the relative richness of Erysipelotrichaceae was high in BC. This observational meta-analysis revealed that the changes in gut microbiota were correlated with BC, and the changes in some primary fecal microbiota might affect the beginning of breast cancer.

Continuous intake of galacto-oligosaccharides containing syrup contributes to maintaining the health of household dogs by modulating their gut microbiota.

Interest is growing in the relationship of the microbiota and intestinal environment with health in companion animals. Galacto-oligosaccharides (GOS), typical prebiotics, are expected to provide benefits in dogs. Previous studies of GOS in dogs have involved dogs with similar rearing conditions and diets, which may have biased the results. We conducted an open study of 26 healthy dogs kept in households with diverse rearing environments in order to evaluate how the intake of a GOS-containing syrup affects the intestinal microbiota and its metabolites. Each dog was fed 1.2-4.8 g of the GOS-containing syrup (GOS 0.5-2.0 g equivalent) for 8 weeks. Fecal microbiota, fecal concentrations of organic acids and putrefactive products, fecal odor, and serum uremic toxin concentrations were evaluated before intake (0 weeks), during the 8-week intake period (4 and 8 weeks), and 4 weeks after intake (12 weeks). The activity of N-benzoyl-DL-arginine peptidase in dental plaque, which may be associated with periodontal disease, was evaluated at 0 and 8 weeks. Continuous intake of GOS resulted in changes in fecal microbiota, with a particularly marked increase in the abundance of Megamonas, which produces propionic acid. Other findings included a significant increase in the fecal acetic, propionic, and n-butyric acid concentrations. Additionally, significant decreases in fecal odor, fecal phenol concentration, and serum indoxyl sulfate concentration. Intake of GOS was also associated with a significant decrease in N-benzoyl-DL-arginine peptidase activity in dental plaques. These results suggest that continuous intake of GOS may contribute to canine health.

Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs.

The breed of pig can affect the diversity and composition of fecal microbiota, but there is a lack of research on the fecal microbiota of hybrid pigs. In this study, feces samples from Chuanxiang black pigs (a hybrid of Tibetan and Duroc pigs) aged 3 days (n = 24), 70 days (n = 31), 10 months (n = 13) and 2 years (n = 30) and Tibetan pigs aged 10 months (n = 14) and 2 years (n = 15) were collected and sequenced by 16S rRNA gene sequencing technology. We also measured the weight of all the tested pigs and found that the 10-month-old and two-year-old Chuanxiang black pigs weighed about three times the weight of Tibetan pigs of the same age. After comparing the genus-level microbiota composition of Tibetan pigs and Chuanxiang black pigs at 10 months and two years of age, we found that Treponema and Streptococcus were the two most abundant bacteria in Chuanxiang black pigs, while Treponema and Chirstensenellaceae_R.7_group were the two most abundant bacteria in Tibetan pigs. Prediction of microbial community function in adult Chuanxiang black pigs and Tibetan pigs showed changes in nutrient absorption, disease resistance, and coarse feeding tolerance. In addition, we also studied the changes in fecal microbiota in Chuanxiang black pigs at 3 days, 70 days, 10 months, and 2 years of age. We found that the ecologically dominant bacteria in fecal microbiota of Chuanxiang black pigs changed across developmental stages. For example, the highest relative abundance of 70-day-old Chuanxiang black pigs at the genus level was Prevotella. We identified specific microbiota with high abundance at different ages for Chuanxiang black pigs, and revealed that the potential functions of these specific microbiota were related to the dominant phenotype such as fast growth rate and strong disease resistance. Our findings help to expand the understanding of the fecal microbiota of hybrid pigs and provide a reference for future breeding and management of hybrid pigs.

Compositional changes in fecal microbiota in a new Parkinson's disease model: C57BL/6-Tg(NSE-haSyn) mice

BackgroundThe gut–brain axis (GBA) in Parkinson's disease (PD) has only been investigated in limited mice models despite dysbiosis of the gut microbiota being considered one of the major treatment targets for neurodegenerative disease. Therefore, this study examined the compositional changes of fecal microbiota in novel transgenic (Tg) mice overexpressing human α-synuclein (hαSyn) proteins under the neuron-specific enolase (NSE) to analyze the potential as GBA model.ResultsThe expression level of the αSyn proteins was significantly higher in the substantia nigra and striatum of NSE-hαSyn Tg mice than the Non-Tg mice, while those of tyrosine hydroxylase (TH) were decreased in the same group. In addition, a decrease of 72.7% in the fall times and a 3.8-fold increase in the fall number was detected in NSE-hαSyn Tg mice. The villus thickness and crypt length on the histological structure of the gastrointestinal (GI) tract decreased in NSE-hαSyn Tg mice. Furthermore, the NSE-hαSyn Tg mice exhibited a significant increase in 11 genera, including Scatolibacter, Clostridium, Feifania, Lachnoclostridium, and Acetatifactor population, and a decrease in only two genera in Ligilactobacillus and Sangeribacter population during enhancement of microbiota richness and diversity.ConclusionsThe motor coordination and balance dysfunction of NSE-hαSyn Tg mice may be associated with compositional changes in gut microbiota. In addition, these mice have potential as a GBA model.

Dynamic changes of fecal microbiota in a weight-change model of Bama minipigs.

Obesity is closely related to gut microbiota, however, the dynamic change of microbial diversity and composition during the occurrence and development process of obesity is not clear. A weight-change model of adult Bama pig (2 years, 58 individuals) was established, and weight gain (27 weeks) and weight loss (9 weeks) treatments were implemented. The diversity and community structures of fecal microbiota (418 samples) was investigated by using 16S rRNA (V3-V4) high-throughput sequencing. During the weight gain period (1~27 week), the alpha diversity of fecal microbiota exhibited a "down-up-down" fluctuations, initially decreasing, recovering in the mid-term, and decreasing again in the later stage. Beta diversity also significantly changed over time, indicating a gradual deviation of the microbiota composition from the initial time point. Bacteroides, Clostridium sensu stricto 1, and Escherichia-Shigella showed positive correlations with weight gain, while Streptococcus, Oscillospira, and Prevotellaceae UCG-001 exhibited negative correlations. In the weight loss period (30~38 week), the alpha diversity further decreased, and the composition structure underwent significant changes compared to the weight gain period. Christensenellaceae R-7 group demonstrated a significant increase during weight loss and showed a negative correlation with body weight. Porphyromonas and Campylobacter were positively correlated with weight loss. Both long-term fattening and weight loss induced by starvation led to substantial alterations in porcine gut microbiota, and the microbiota changes observed during weight gain could not be recovered during weight loss. This work provides valuable resources for both obesity-related research of human and microbiota of pigs.

Compound Bacillus alleviates diarrhea by regulating gut microbes, metabolites, and inflammatory responses in pet cats

BackgroundPet cats frequently have diarrhea in their daily life. Bacillus has a protective role that has crucial beneficial functions on intestinal homeostasis. The aim of this research was to investigate the effects of the compound Bacillus on the prevention of diarrhea, microbiota and metabolism in pet cats. A total of 20 pet cats (1–2 years old, 3.91 ± 0.92 kg) were randomly divided into two groups and fed with a basal diet (Control group), or a basal diet supplemented with 3 × 109 CFU/kg compound Bacillus (Probiotics group). The experiment lasted 33 days.ResultsResults showed that the compound Bacillus significantly reduced the rate of soft stools and diarrhea in pet cats compared with the control group (P < 0.05, n = 10). Meanwhile, compared with the control group, the probiotics group significantly decreased the content of IL-1β and IL-6 and significantly increased IL-10 (P < 0.05, n = 6) in the serum. In addition, feeding probiotics significantly increased the abundance of p_Patescibacter and g_Plectosphaerella, decreased the abundance of p_Firmicutes, p_Gemmatimonadetes, g_Ruminococcaceae_UCG-005, g_Ascochytahe and g_Saccharomyces in the feces of the pet cats (P < 0.05, n = 6). And it also can significantly increase the content of total SCFAs, acetic acid and butyric acid in the feces (P < 0.05, n = 6). The fecal and serum metabolomics analyses revealed that most fecal and serum compounds were involved in metabolism, particularly in chemical structure transformation maps and amino acid metabolism. Also, eugenitol and methyl sulfate were the most significantly increased serum metabolites, and log2FC were 38.73 and 37.12, respectively. Pearson’s correlation analysis showed that changes in serum metabolism and fecal microbiota were closely related to immune factors. There was also a strong correlation between serum metabolites and microbiota composition.ConclusionsThe results of this research highlight the potential of the compound Bacillus as a dietary supplement to alleviate diarrhea in pet cats.

Akkermansia muciniphila supplementation improves glucose tolerance in intestinal Ffar4 knockout mice during the daily light to dark transition.

Alterations in the intestinal environment are associated with various diseases, and FFAR4 is abundantly enriched in the intestine, where it has been shown to have the ability to regulate intestinal hormone secretion and intestinal microbiota; here, we confirmed previous reports. Meanwhile, we found that intestinal FFAR4 regulates glucagon-like peptide 1 secretion by decreasing Akkermansia muciniphila abundance and show that such change is associated with the level of glucose utilization at ZT12 in mice. Intestinal FFAR4 deficiency leads to severely impaired glucose tolerance at the ZT12 moment in mice, and Akkermansia muciniphila supplementation ameliorates the abnormal glucose utilization at the ZT12 moment caused by FFAR4 deficiency, which is very similar to the dawn phenomenon in diabetic patients. Collectively, our data suggest that intestinal Ffar4 deteriorates glucose tolerance at the daily light to dark transition by affecting Akkermansia muciniphila.

An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial.

Probiotic supplements, by definition, provide a benefit to the host, but few studies have investigated the effect of probiotic supplements in healthy adult populations. The present, single arm, open label clinical trial, evaluated compositional and functional changes in the fecal microbiome of healthy adults after supplementation with a 14-strain probiotic. We analysed the effect of a 14-strain probiotic blend (Bacillus subtilis NCIMB 30223, Bifidobacterium bifidum NCIMB 30179, B. breve NCIMB 30180, B. infantis NCIMB 30181, B. longum NCIMB 30182, Lactobacillus helveticus NCIMB 30184, L. delbrueckii subsp. bulgaricus NCIMB 30186, Lacticaseibacillus paracasei NCIMB 30185, Lactiplantibacillus plantarum NCIMB 30187, Lacticaseibacillus rhamnosus NCIMB 30188, L. helveticus NCIMB 30224, Lactobacillus salivarius NCIMB 30225, Lactococcus lactis subsp. lactis NCIMB 30222, and Streptococcus thermophilus NCIMB 30189), on the faecal microbiota of healthy young adults (n=41) in a single arm study. The adults consumed 4 capsules daily of the 14 strain blend(8 billion colony forming units/day) for 8 weeks. Compositional and functional changes in faecal microbiota before and after supplementation were assessed using shotgun metagenomic sequencing. Fasting breath analysis, faecal biochemistry and bowel habits were also assessed. In healthy adult participants, no significant changes to the overall alpha- or beta-diversity was observed after 8 weeks of multi-strain probiotic supplementation. However, in a simplified model that considered only time and individual differences, significant decreases (p < 0.05) in family Odoribacteraceae and Bacteroidaceae abundance and a significant increase (p < 0.05) in genus Megamonas abundance were observed. At a functional level, there were significant changes in functional gene abundance related to several functional pathways, including phenylalanine metabolism, O-antigen nucleotide sugar biosynthesis, bacterial chemotaxis, and flagellar assembly. No significant changes in stool form or frequency, fecal biochemistry, or methane and hydrogen breath tests were observed. In healthy young adults, overall alpha- and beta-diversity did not change in response to probiotic intake even though modest compositional changes at the family and genus level were observed. However, at functional level, results identified changes in gene abundance for several functional pathways.

Evaluating the Potential of Casein Glycomacropeptide in Adult Irritable Bowel Syndrome Management: A Pilot Study.

Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that affects 10-15% of the global population and presents symptoms such as abdominal discomfort, bloating and altered bowel habits. IBS is believed to be influenced by gut microbiota alterations and low-grade inflammation. Bovine kappa-casein glycomacropeptide (GMP), a bioactive dairy-derived peptide, possesses anti-adhesive, prebiotic and immunomodulatory properties that could potentially benefit IBS patients. This pilot study investigated the effects of daily supplementation with 30 g of GMP for three weeks on gut health in five people with IBS. We assessed alterations in gut microbiota composition, fecal and blood inflammatory makers, and gut-related symptoms before, during and after the GMP feeding period. The results revealed no changes in fecal microbiota, subtle effects on systemic and intestinal immune makers, and no changes in gut-related symptoms during and after the GMP supplementation. Further research is needed to assess the potential benefits of GMP in IBS patients, including the examination of dosage and form of GMP supplementation.

Fecal microbial and metabolic characteristics of swine from birth to market.

Recently, the research on pig intestinal microbiota has become a hot topic in the field of animal husbandry. There are few articles describing the dynamic changes of porcine fecal microbiota and metabolites at different time points from birth to market. In the present study, 381 fecal samples were collected from 633 commercial pigs at 7 time points, including the 1st day, the 10th day, the 25th day, the 45th day, the 70th day, the 120th day, and the 180th day after the birth of swine, were used for microbiome analysis by Illumina MiSeq sequencing methods while 131 fecal samples from 3 time points, the 10th day, the 25th day, and 70th day after birth, were used for metabolome analysis by LC-MS methods. For the microbiome analysis, the fecal microbial richness increased over time from day 1 to 180 and the β-diversity of fecal microbiota was separated significantly at different time points. Firmicutes were the main phyla from day 10 to 180, followed by Bacteroides. The abundance of Lactobacillus increased significantly on day 120 compared with the previous 4 time points. From day 120 to day 180, the main porcine fecal microbes were Lactobacillus, Clostridium_sensu_stricto_1, Terrisporobacter and Streptococcus. Clostridium_sensu_stricto_1 and Terrisporobacter increased over time, while Lactobacillus, Escherichia-Shigella, Lachnoclostridium decreased with the time according to the heatmap, which showed the increase or decrease in microbial abundance over time. For the metabolome analysis, the PLS-DA plot could clearly distinguish porcine fecal metabolites on day 10, 25, and 70. The most different metabolic pathways of the 3 time points were Tryptophan metabolism, Sphingolipid signaling pathway, Protein digestion and absorption. Some metabolites increased significantly over time, such as Sucrose, L-Arginine, Indole, 2,3-Pyridinedicarboxylic acid and so on, while D-Maltose, L-2-Aminoadipic acid, 2,6-diaminohexanoic acid, L-Proline were opposite. The correlation between fecal metabolites and microbiota revealed that the microbes with an increasing trend were positively correlated with the metabolites affecting the tryptophan metabolic pathway from the overall trend, while the microbes with a decreasing trend were opposite. In addition, the microbes with an increasing trend were negatively correlated with the metabolites affecting the lysine pathway. In conclusion, this study elucidated the dynamic changes of porcine fecal microbiota and metabolites at different stages from birth to market, which may provide a reference for a comprehensive understanding of the intestinal health status of pigs at different growth stages.

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients.MethodsFrom March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR.ResultsAlthough similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients.ConclusionsOverall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology.Trial registrationCER-VD 2020–00755 (05.05.2020) & 2017–01820 (08.06.2018).

Analysis of Fecal Microbial Changes in Young Calves Following Bovine Rotavirus Infection.

The objective of the present study was to identify changes in fecal microbiota and predict the functional features of healthy calves and those infected with rotavirus over time. Six Holstein calves (average body weight 43.63 ± 1.19 kg, age-matched within 5-7 d) were randomly selected and distributed into two groups which contained three calves each. Fecal samples were taken 3 days before inoculation and on days 1 and 7 post-inoculation. The 16S rRNA gene amplicon sequencing was performed. Bacterial diversity tended to decrease in the rota group, as indicated by the alpha (evenness, p = 0.074 and Shannon, p = 0.055) and beta (Bray-Curtis dissimilarity, p = 0.099) diversity at 1 day post-inoculation. Differences in the bacterial taxa between healthy and rota-infected calves were detected using a linear discriminant analysis effect size (LDA > 2.0, p < 0.05). Rota calves had a higher abundance of certain bacterial taxa, such as Enterococcus, Streptococcus, and Escherichia-Shigella, and a lower abundance of bacteria that contribute to the production of short-chain fatty acids, such as Alistipes, Faecalibacterium, Pseudoflavonifractor, Subdoligranulum, Alloprevotella, Butyricicoccus, and Ruminococcus, compared to the healthy calves. The observed changes in the fecal microbiota of the rota-infected group compared to the healthy group indicated potential dysbiosis. This was further supported by significant differences in the predicted functional metagenomic profiles of these microbial communities. We suggest that calves infected with bovine rotavirus had bacterial dysbiosis, which was characterized by lower diversity and fewer observed genera than the fecal microbiota of healthy calves.