Gut Microbiota, Fusobacteria, and Colorectal Cancer

Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis

BACKGROUND/PURPOSE(S)

The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation.

METHODS

We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples.

RESULTS

Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA.

CONCLUSION

Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.

Exploring Functional Products and Early-Life Dynamics of Gut Microbiota

Research on the microbiome has progressed from identifying specific microbial communities to exploring how these organisms produce and modify metabolites that impact a wide range of health conditions, including gastrointestinal, metabolic, autoimmune, and neurodegenerative diseases. This review provides an overview of the bacteria commonly found in the intestinal tract, focusing on their main functional outputs. We explore biomarkers that not only indicate a well-balanced microbiota but also potential dysbiosis, which could foreshadow susceptibility to future health conditions. Additionally, it discusses the establishment of the microbiota during the early years of life, examining factors such as gestational age at birth, type of delivery, antibiotic intake, and genetic and environmental influences. Through a comprehensive analysis of current research, this article aims to enhance our understanding of the microbiota's foundational development and its long-term implications for health and disease management.

Campylobacter infection of young children in Colombia and its impact on the gastrointestinal environment

Campylobacter infections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low-and-middle income countries. It remains unclear how Campylobacter impacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well characterized clinical cohorts in diverse settings. In this study, we analyzed the fecal microbiota and the metabolomic and micronutrient profiles of asymptomatic and symptomatic pediatric patients in Colombia that were either infected or uninfected with Campylobacter during a case-controlled study on acute diarrheal disease. Here, we report that the microbiome of Campylobacter- infected children only changed in their abundance of Campylobacter spp. despite the inclusion of children with or without diarrhea. In addition to increased Campylobacter, computational models were used to identify fecal metabolites that were associated with Campylobacter infection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggest that colonocyte metabolism are impacted during infection. Despite changes to the fecal metabolome, the concentrations of intestinal minerals and trace elements were not significantly impacted by Campylobacter infection, but were elevated in uninfected children with diarrhea.

Importance

Gastrointestinal infection with pathogenic Campylobacter species has long been recognized as a significant cause of human morbidity. Recently, it has been observed that pediatric populations in low-and-middle income countries are uniquely impacted by these organisms in that infected children can be persistently colonized, develop enteric dysfunction, and exhibit reduced development and growth. While the association of Campylobacter species with these long-term effects continues to emerge, the impact of infection on the gastrointestinal environment of these children remains uncharacterized. To address this knowledge gap, our group leveraged clinical samples collected during a previous study on gastrointestinal infections in pediatric patients to examine the fecal microbiota, metabolome, and micronutrient profiles of those infected with Campylobacter species, and found that the metabolome was impacted in a way that suggests gastrointestinal cell metabolism is affected during infection, which is some of the first data indicating how gastrointestinal health in these patients may be affected.

Synergistic Effect of Dietary Supplementation with Sodium Butyrate, β-Glucan and Vitamins on Growth Performance, Cortisol Level, Intestinal Microbiome and Expression of Immune-Related Genes in Juvenile African Catfish (Clarias gariepinus)

The effect of dietary supplementation with sodium butyrate, β-glucan and vitamins (A, D3, E, K, C) on breeding indicators and immune parameters of juvenile African catfish was examined. The fish were fed with unenriched (group C) and enriched feed with a variable proportion of sodium butyrate/β-glucan, and constant content of vitamins (W1-W3). After the experiment, blood and the middle gut were collected. The microbiome of the gut was determined using Next Generation Sequencing (NGS). Liver tissue was collected for determination of expression of immune-related genes (HSP70, IL-1β, TNFα). W2 and W3 were characterized by the most favorable values of breeding indicators (p < 0.05). The highest blood cortisol concentration was in group C (71.25 ± 10.45 ng/mL), and significantly the lowest in W1 (46.03 ± 7.01 ng/ mL) (p < 0.05). The dominance of Cetobacterium was observed in all study groups, with the largest share in W3 (65.25%) and W1 (61.44%). Gene expression showed an increased number of HSP70 genes in W1. IL-1β and TNFα genes peaked at W3. The W3 variant turns out to be the most beneficial supplementation, due to the improvement of breeding and immunological parameters. The data obtained can be used to create a preparation for commercial use in the breeding of this species.

Prevalence and implications of pKs-positive Escherichia coli in colorectal cancer

Colorectal cancer (CRC) remains a significant global health concern, necessitating continuous investigation into its etiology and potential risk factors. Recent research has shed light on the potential role of pKs-positive Escherichia coli (pKs + E. coli) and colibactin in the development and progression of CRC. Therefore, this review aimed to provide an updated analysis of the prevalence and implications of pKs + E. coli in colorectal cancer. We conducted a literature review search in major scientific databases to identify relevant studies exploring the association between pKs + E. coli and CRC. The search strategy included studies published up to the present date, and articles were carefully selected based on predefined inclusion criteria. Thus, the present study encompasses scientific evidence from clinical and epidemiological studies supporting the presence of pKs + E. coli in CRC patients, demonstrating a consistent and significant association in multiple studies. Furthermore, we highlighted the potential mechanisms by which colibactin may promote tumorigenesis and cancer progression within the colorectal mucosa, including the production of genotoxic virulence factors. Additionally, we explored current diagnostic methods for detecting pKs + E. coli in clinical settings, emphasizing the importance of accurate identification. Moreover, we discussed future strategies that could utilize the presence of this strain as a biomarker for CRC diagnosis and treatment. In conclusion, this review consolidated existing evidence on the prevalence and implications of pKs + E. coli in colorectal cancer. The findings underscore the importance of further research to elucidate the precise mechanisms linking this strain to CRC pathogenesis and to explore its potential as a therapeutic target or diagnostic marker. Ultimately, a better understanding of the role of pKs + E. coli in CRC may pave the way for innovative strategies in CRC management and patient care.

Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone

Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.

Effects of dietary Nisin on growth performance, immune function, and gut health of broilers challenged by Clostridium perfringens

Nisin (Ni) is a polypeptide bacteriocin produced by lactic streptococci (probiotics) that can inhibit the majority of gram-positive bacteria, and improve the growth performance of broilers, and exert antioxidative and anti-inflammatory properties. The present study investigated the potential preventive effect of Nisin on necrotic enteritis induced by Clostridium perfringens (Cp) challenge. A total of 288 Arbor Acres broiler chickens of 1-d-olds were allocated using 2 × 2 factorial arrangement into four groups with six replicates (12 chickens per replicate), including: (1) control group (Con, basal diet), (2) Cp challenge group (Cp, basal diet + 1.0 × 108 CFU/mL Cp), (3) Ni group (Ni, basal diet + 100 mg/kg Ni), and (4) Ni + Cp group (Ni + Cp, basal diet + 100 mg/kg Ni + 1.0 × 108 CFU/mL Cp). The results showed that Cp challenge decreased the average daily gain (ADG) of days 15 to 21 (P<0.05) and increased interleukin-6 (IL-6) content in the serum (P < 0.05), as well as a significant reduction in villus height (VH) and the ratio of VH to crypt depth (VCR) (P<0.05) and a significant increase in crypt depth (CD) of jejunum (P<0.05). Furthermore, the mRNA expressions of Occludin and Claudin-1 were downregulated (P<0.05), while the mRNA expressions of Caspase3, Caspase9, Bax, and Bax/Bcl-2 were upregulated (P<0.05) in the jejunum. However, the inclusion of dietary Ni supplementation significantly improved body weight (BW) on days 21 and 28, ADG of days 15 to 21 (P<0.05), decreased CD in the jejunum, and reduced tumor necrosis factor-α (TNF-α) content in the serum (P<0.05). Ni addition upregulated the mRNA levels of Claudin-1 expression and downregulated the mRNA expression levels of Caspase9 in the jejunum (P<0.05). Moreover, Cp challenge and Ni altered the cecal microbiota composition, which manifested that Cp challenge decreased the relative abundance of phylum Fusobacteriota and increased Shannon index (P<0.05) and the trend of phylum Proteobacteria (0.05 Collapse

Key Words

• Clostridium perfringens
• broiler
• gut health
• necrotic enteritis
• nisin

Collapse

MESH Headings

• Animals
• Clostridium perfringens
• Chickens
• Intestines
• Clostridium Infections/prevention & control
• Clostridium Infections/veterinary
• Clostridium Infections/microbiology
• Nisin/pharmacology
• Claudin-1
• bcl-2-Associated X Protein/pharmacology
• Diet/veterinary
• RNA, Messenger/genetics
• Immunity
• Poultry Diseases/microbiology
• Dietary Supplements
• Animal Feed/analysis

Collapse

Grants Collapse

Affiliation(s)

Hua Yuan College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Guangdong Bai College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China College of Animal Science and Technology, Southwest University, Chongqing 400715, China
Yu Lin College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Xilong Yu College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Qinghui Yang College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Renkai Dou College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Hao Sun College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Zeyu Zhao College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Zhongyu Li College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Zhihui Chen College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
Liangmei Xu College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China

Collapse

Gut microbiota perturbations during larval stages in Bufo gargarizans tadpoles after Cu exposure with or without the presence of Pb

Cu and Pb are ubiquitous environmental contaminants, but there is limited information on their potential impacts on gut microbiota profile in anuran amphibians at different developmental stages during metamorphosis. In this study, Bufo gargarizans tadpoles were chronically exposed to Cu alone or Cu combined with Pb from Gs26 throughout metamorphosis. Morphology of tadpoles, histological characteristic and bacterial community of intestines were evaluated at three developmental stages: Gs33, Gs36, and Gs42. Results showed that Cu and Cu + Pb exposure caused various degrees of morphological and histological changes in guts at tested three stages. In addition, bacterial richness and diversity in tadpoles especially at Gs33 and Gs42 were disturbed by Cu and Cu + Pb. Beta diversity demonstrated that the bacterial community structures were influenced by both heavy metals exposure and developmental stages. Alterations in taxonomic composition were characterized by increased abundance of Proteobacteria and Firmicutes, reduction of Fusobacteriota, as well as decreased Cetobacterium and increased C39 at all three stages. Overall, response of gut bacterial diversity and composition to Cu stress depends on the developmental stage, while the altered patterns of bacterial community at Cu stress could be modified further by the presence of Pb. Moreover, predicted metabolic disorders were associated with shifts in bacterial community, but needs integrated information from metagenomic and metatranscriptomic analyses. These results contribute to the growing body of research about potential ecotoxicological effects of heavy metals on amphibian gut microbiota during metamorphosis.

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.

Metagenomic and metabolomic analysis of changes in intestinal contents of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus at different culture water temperatures

Infectious hematopoietic necrosis (IHN) is a major disease that limits the culture of rainbow trout. In practical production, it has been found that the temperature of the culture water is a crucial factor affecting its mortality. Currently, little is known about how temperature affects the immune response of rainbow trout gut microbiota and metabolites to IHNV. In this study, our main objective is to analyze the changes in gut microorganisms of rainbow trout (juvenile fish with a consistent genetic background) after 14 days of infection with IHNV (5 × 105 pfu/fish) at 12-13°C (C: injected with saline, A: injected with IHNV) and 16-17°C (D: injected with saline, B: injected with IHNV) using metagenomic and metabolomic analyses, and to screen for probiotics that are effective against IHNV. The results showed that infection with IHNV at 12-13°C caused Eukaryote loss. Compared to Group C, Group A showed a significant increase in harmful pathogens, such as Yersiniaceae, and a significant alteration of 4,087 gut metabolites. Compared to group D, group B showed a significant increase in the abundance of Streptococcaceae and Lactococcus lactis, along with significant changes in 4,259 intestinal metabolites. Compared with their respective groups, the levels of two immune-related metabolites, 1-Octadecanoyl-glycero-3-phosphoethanolamine and L-Glutamate, were significantly upregulated in groups A and B. Compared to group B, Group A showed significantly higher pathogenic bacteria including Aeromonas, Pseudomonas, and Yersiniaceae, while group B showed a significant increase in Streptococcaceae and Lactococcus lactis. Additionally, there were 4,018 significantly different metabolites between the two groups. Interestingly, 1-Octadecanoyl-sn-glycero-3-phosphoethanolamine and L-Glutamate were significantly higher in group A than in group B. Some of the different metabolites in C vs. A are correlated with Fomitopsis pinicola, while in D vs. B they were correlated with Lactococcus raffinolactis, and in A vs. B they were correlated with Hypsizygus marmoreus. This study exposed how rainbow trout gut microbiota and metabolites respond to IHNV at different temperatures, and screens beneficial bacteria with potential resistance to IHN, providing new insights and scientific basis for the prevention and treatment of IHN.

From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes

The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.

Evidence for proton-pump inhibitor (PPI)-associated dysbiosis in metabolically unhealthy obesity

Obesity adversely impacts millions of American adults by predisposing them to significant health risks and further complications. Obesity is differentiated into two groups: metabolically healthy and metabolically unhealthy. In contrast to metabolically healthy counterparts, obese individuals who are metabolically unhealthy display hallmark symptoms of metabolic syndrome (e.g., hypertension, dyslipidemia, hyperglycemia, abdominal obesity). Gastroesophageal reflux disease (GERD) commonly occurs in all obese populations, as do poor dietary habits. Proton-pump inhibitors (PPIs), due to their wide availability, are most often used to treat GERD-related heartburn and other symptoms. Here, we review the evidence on how poor diet as well as short- and long-term use of PPIs adversely affect the gastrointestinal microbiota to cause dysbiosis. Key components of dysbiosis-induced metabolically unhealthy obesity (MUO) associated with PPI use include "leaky gut," systemic low-grade inflammation, and reduced amounts of short-chain fatty acids (SCFAs) such as butyrate that promote metabolic health. The benefit of using probiotics to mitigate PPI-induced dysbiosis and MUO is also discussed.

Implication of Obesity and Gut Microbiome Dysbiosis in the Etiology of Colorectal Cancer

The complexity and variety of gut microbiomes within and among individuals have been extensively studied in recent years in connection to human health and diseases. Our growing understanding of the bidirectional communication between metabolic diseases and the gut microbiome has also highlighted the significance of gut microbiome dysbiosis in the genesis and development of obesity-related cancers. Therefore, it is crucial to comprehend the possible role of the gut microbiota in the crosstalk between obesity and colorectal cancer (CRC). Through the induction of gut microbial dysbiosis, gut epithelial barrier impairment, metabolomic dysregulation, chronic inflammation, or dysregulation in energy harvesting, obesity may promote the development of colorectal tumors. It is well known that strategies for cancer prevention and treatment are most effective when combined with a healthy diet, physical activity, and active lifestyle choices. Recent studies also suggest that an improved understanding of the complex linkages between the gut microbiome and various cancers as well as metabolic diseases can potentially improve cancer treatments and overall outcomes. In this context, we herein review and summarize the clinical and experimental evidence supporting the functional role of the gut microbiome in the pathogenesis and progression of CRC concerning obesity and its metabolic correlates, which may pave the way for the development of novel prognostic tools for CRC prevention. Therapeutic approaches for restoring the microbiome homeostasis in conjunction with cancer treatments are also discussed herein.

Exploratory Evaluation of Neopterin and Chitotriosidase as Potential Circulating Biomarkers for Colorectal Cancer

Chronic inflammation is demonstrated to play a direct role in carcinogenesis. Our exploratory study aimed to assess the potential added value of two inflammation biomarkers, chitotriosidase and neopterin, in follow-up evaluation of patients with colorectal cancer (CRC). An observational exploratory study was conducted. Patients with CRC and matched controls (1:1, age, sex, and living environment) were evaluated. The patients with CRC (CRC group) and controls were assessed at baseline (before surgical intervention for patients with CRC). Patients with CRC were also evaluated at 1-year follow-up. Significantly more patients with blood group A (54.5% vs. 25.0%) and smokers (50.0% vs. 22.7%) were in the CRC group. The serum values of chitotriosidase and neopterin were higher in CRC patients than in controls, but only neopterin reached the conventional level of statistical significance (p-value = 0.015). The circulating chitotriosidase and neopterin values decreased significantly at 1-year follow-up (p-value < 0.0001). Patients with higher N- and M-stage showed statistically significant higher levels of chitotriosidase and neopterin at baseline and 1-year follow-up (p-values < 0.03). Circulating chitotriosidase levels also showed statistically significant differences regarding baseline and 1-year follow-up on patients with CRC and different differentiation grades (p-values < 0.02). The circulating levels of neopterin significantly decreased at 1-year follow-up, indicating its potential as a prognostic marker. The circulating values of chitotriosidase and neopterin exhibit significant differences in patients with than without recurrences. Our results support further evaluation of chitotriosidase and neopterin as prognostic markers in patients with CRC.

E2F1 inhibits cellular senescence and promotes oxaliplatin resistance in colorectal cancer

Background

Doctors have always been overwhelmed by tumor drug resistance because it is a major challenge in the clinical treatment of tumors. Cellular senescence has a strong relationship with the development of tumor drug resistance. Herein, we aimed to explore new regulatory factors involved in the aging process of colorectal cancer (CRC) cells and assess the effect of cellular senescence on CRC drug resistance.

Methods

Genes associated with cellular senescence for anticipating regulatory factors were first used, and the regulatory molecules of survival significance were then identified based on the results of public database analysis. The effects of E2F translation factor 1 (E2F1) on CRC cell viability, invasion, migration, and cellular senescence processes were assessed through 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide (MTT), 5-Ethynyl-2'-deoxyuridine (EdU), Transwell, scar repairining, β-galactosidase staining, and cell immunofluorescence assays, respectively. Overexpression or silencing plasmids were used for transfecting HCT116 or OXA-HCT116 to assess the effect of E2F1 on the senescence process and drug resistance in CRC cells.

Results

On combining the database analysis results with those of our studies, we found that E2F1 was a critical regulator of cellular senescence in CRC. In the in vitro experiments, the E2F1 overexpression significantly stimulated the proliferation, invasion, and migration of CRC cells and even reduced oxaliplatin-induced senescence, further enhancing their resistance to oxaliplatin. Conversely, the tumorigenesis of colorectal cancer was repressed after the suppression of E2F1. Furthermore, CRC cells, which were otherwise resistant to oxaliplatin, also showed senescent phenotypes.

Conclusions

Our results suggest that E2F1 suppresses the aging of CRC cells and tumor cells develop resistance to oxaliplatin through high E2F1 expression. Moreover, E2F1 may act as a possible target for oxaliplatin resistance studies.

Characterization of the Gut Microbiota in Urban Thai Individuals Reveals Enterotype-Specific Signature

Gut microbiota play vital roles in human health, utilizing indigestible nutrients, producing essential substances, regulating the immune system, and inhibiting pathogen growth. Gut microbial profiles are dependent on populations, geographical locations, and long-term dietary patterns resulting in individual uniqueness. Gut microbiota can be classified into enterotypes based on their patterns. Understanding gut enterotype enables us to interpret the capability in macronutrient digestion, essential substance production, and microbial co-occurrence. However, there is still no detailed characterization of gut microbiota enterotype in urban Thai people. In this study, we characterized the gut microbiota of urban Thai individuals by amplicon sequencing and classified their profiles into enterotypes, including Prevotella (EnP) and Bacteroides (EnB) enterotypes. Enterotypes were associated with lifestyle, dietary habits, bacterial diversity, differential taxa, and microbial pathways. Microbe-microbe interactions have been studied via co-occurrence networks. EnP had lower α-diversities than those in EnB. A correlation analysis revealed that the Prevotella genus, the predominant taxa of EnP, has a negative correlation with α-diversities. Microbial function enrichment analysis revealed that the biosynthesis pathways of B vitamins and fatty acids were significantly enriched in EnP and EnB, respectively. Interestingly, Ruminococcaceae, resistant starch degraders, were the hubs of both enterotypes, and strongly correlated with microbial diversity, suggesting that traditional Thai food, consisting of rice and vegetables, might be the important drivers contributing to the gut microbiota uniqueness in urban Thai individuals. Overall findings revealed the biological uniqueness of gut enterotype in urban Thai people, which will be advantageous for developing gut microbiome-based diagnostic tools.

Distinct changes in the colonic microbiome associated with acute diverticulitis

AIM

The pathogenesis of acute diverticulitis (AD) remains incompletely understood, despite it being one of the most common gastrointestinal conditions worldwide. The aim of this study was to investigate the role of the colonic microbiome in the pathogenesis of AD.

METHOD

A prospective case-control study was performed, comparing the microbiome of AD patients with that of controls, using 16S rRNA sequencing of rectal swab samples.

RESULTS

The microbiome of individuals with AD showed lower diversity than that of controls. There were significant compositional differences observed, with a lower abundance of commensal bacterial families and genera such as Lachnospiraceae, Ruminococcus and Faecalibacterium in AD patients compared with controls, and there was an increase in several genera with known pathogenic roles including Fusobacteria, Prevotella and Paraprevotella.

CONCLUSION

This is the largest study to date to examine the microbiota of AD patients, and adds evidence to the proposed hypothesis that alterations in the colonic microbiome play a role in the pathogenesis of AD.

Maternal obesity during pregnancy leads to derangements in one-carbon metabolism and the gut microbiota: implications for fetal development and offspring wellbeing

A healthy diet before and during pregnancy is beneficial in acquiring essential B vitamins involved in 1-carbon metabolism, and in maintaining a healthy gut microbiota. Each play important roles in fetal development, immune-system remodeling, and pregnancy-nutrient acquisition. Evidence shows that there is a reciprocal interaction between the one-carbon metabolism and the gut microbiota given that dietary intake of B vitamins has been shown to influence the composition of the gut microbiota, and certain gut bacteria also synthesize B vitamins. This reciprocal interaction contributes to the individual's overall availability of B vitamins and, therefore, should be maintained in a healthy state during pregnancy. There is an emerging consensus that obese pregnant women often have derangements in 1-carbon metabolism and gut dysbiosis owing to high intake of nutritiously poor foods and a chronic systemic inflammatory state. For example, low folate and vitamin B₁₂ in obese women coincide with the decreased presence of B vitamin-producing bacteria and increased presence of inflammatory-associated bacteria from approximately mid-pregnancy. These alterations are risk factors for adverse pregnancy outcomes, impaired fetal development, and disruption of fetal growth and microbiota formation, which may lead to potential long-term offspring metabolic and neurologic disorders. Therefore, preconceptional and pregnant obese women may benefit from dietary and lifestyle counseling to improve their dietary nutrient intake, and from monitoring their B vitamin levels and gut microbiome by blood tests and microbiota stool samples. In addition, there is evidence that some probiotic bacteria have folate biosynthetic capacity and could be used to treat gut dysbiosis. Thus, their use as an intervention strategy for obese women holds potential and should be further investigated. Currently, there are many knowledge gaps concerning the relationship between one-carbon metabolism and the gut microbiota, and future research should focus on intervention strategies to counteract B vitamin deficiencies and gut dysbiosis in obese pregnant women, commencing with the use of probiotic and prebiotic supplements.

Effects of in situ experimental selenium exposure on finescale dace (Phoxinus neogaeus) gut microbiome

Selenium (Se) is an environmental contaminant of global concern that can cause adverse effects in fish at elevated levels. Fish gut microbiome play essential roles in gastrointestinal function and host health and can be perturbed by environmental contaminants, including metals and metalloids. Here, an in-situ Se exposure of female finescale dace (Phoxinus neogaeus) using mesocosms was conducted to determine the impacts of Se accumulation on the gut microbiome and morphometric endpoints. Prior to this study, the gut microbiome of finescale dace, a widespread Cyprinid throughout North America, had not been characterized. Exposure to Se caused a hormetic response of alpha diversity of the gut microbiome, with greater diversity at the lesser concentration of 1.6 μg Se/L, relative to that of fish exposed to the greater concentration of 5.6 μg Se/L. Select gut microbiome taxa of fish were differentially abundant between aqueous exposure concentrations and significantly correlated with liver-somatic index (LSI). The potential effects of gut microbiome dysbiosis on condition of wild fish might be a consideration when assessing adverse effects of Se in aquatic environments. More research regarding effects of Se on field-collected fish gut microbiome and the potential adverse effects or benefits on the host is warranted.

Portulaca oleracea polysaccharides reduce serum lipid levels in aging rats by modulating intestinal microbiota and metabolites

Metabolic diseases characterized by dyslipidemia are common health problems for elderly populations. Dietary fiber intake is inversely associated with the risk of dyslipidemia. This study investigated the effects of Portulaca oleracea polysaccharide (POP) on the intestinal microbiota and its metabolites in aging rats using 16S rRNA sequencing and metabolomics techniques. Our results showed that POPs reduced the ratio of Firmicutes/Bacteroidetes (F/B), relative abundance of Fusobacteria, and levels of triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), alanine aminotransferase (ALT), and gamma-glutamyl transferase (γ-GT) in the serum of aging rats. POP supplementation also reduced 5beta-cholestane-3alpha,7alpha,12alpha,25-tetrol, and vaccenic acid concentrations in lipids and lipoid-like molecules, while soyasapogenol E and monoacylglycerol (MG) (24:0/0:0/0:0) levels increased. This study demonstrated that POP’s beneficial effects on lipid levels in aging rats might be partially attributable to the modification of gut microbiota and related metabolites.

Fusobacterium nucleatum: a new player in regulation of cancer development and therapeutic response

A dysbiosis in microbial diversity or functionality can promote disease development. Emerging preclinical and clinical evidence emphasizes the interplay between microbiota and both disease evolution and the treatment response of different cancers. One bacterium that has garnered much attention in a few cancer microbiota studies is Fusobacterium nucleaum (Fn). To provide updated knowledge of the functional role of Fn in cancer prevention and management, this review summarizes the relationship among Fn, cancer, and chemoimmunotherapy response, with the potential mechanisms of action also intensively discussed, which will benefit the development of strategies to prevent or treat cancer via Fn-based therapeutic interventions.

Dysbiosis in Children With Neurological Impairment and Long-Term Enteral Nutrition

Severe neurological impairment (NI) is often accompanied by the need for artificial nutritional support, normally provided enterally (enteral nutrition [EN]) to ensure growth, counteract morbidity and mortality, and improve quality of life. On the other hand, long-term EN (LTEN) may contribute to the establishment, or exacerbation, of gastrointestinal disorders that may lead to malnutrition, which in turn is associated with alterations in gut microbiota (GM) composition and functional capacities. To the best of our knowledge, we investigated, for the first time in this study, the consequences of LTEN in a pediatric population in this pathological context. Using amplicon sequencing, we compared the fecal microbiota of a pediatric population suffering from severe NI and under LTEN to that of sex- and age-matched controls. The two groups presented evident differences in GM composition and a consistent differential clustering. In general, the taxonomic picture in NI children under LTEN seemed to mirror a profound dysbiotic condition, in which anti-inflammatory taxa appear severely depleted (among others, the Clostridiales families of Lachnospiraceae and Ruminococcaceae, and, within the latter, Faecalibacterium spp. and Gemmiger spp.), while known pathobionts (Gammaproteobacteria and Klebsiella) or emerging pathogens (e.g., Synergistales, Cloacibacillus, and Fusobacterium) were significantly enriched. Our data suggest that LTEN has a significant impact on the GM taxonomic composition in NI children. Even if other factors are probably at work, such as the bidirectional interaction between gastrointestinal impairment/immaturity and the central nervous system (CNS), the assumption of drugs, and physical inactivity, these data define possible routes and targets to try to alleviate this dysbiosis, with a view to better management of these patients and an improvement in their quality of life.

Metagenomics and artificial intelligence in the context of human health

Human microbiome is ubiquitous, dynamic, and site-specific consortia of microbial communities. The pathogenic nature of microorganisms within human tissues has led to an increase in microbial studies. Characterization of genera, like Streptococcus, Cutibacterium, Staphylococcus, Bifidobacterium, Lactococcus and Lactobacillus through culture-dependent and culture-independent techniques has been reported. However, due to the unique environment within human tissues, it is difficult to culture these microorganisms making their molecular studies strenuous. MGs offer a gateway to explore and characterize hidden microbial communities through a culture-independent mode by direct DNA isolation. By function and sequence-based MGs, Scientists can explore the mechanistic details of numerous microbes and their interaction with the niche. Since the data generated from MGs studies is highly complex and multi-dimensional, it requires accurate analytical tools to evaluate and interpret the data. Artificial intelligence (AI) provides the luxury to automatically learn the data dimensionality and ease its complexity that makes the disease diagnosis and disease response easy, accurate and timely. This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.

Association of Gut Microbiota and Biochemical Features in a Chinese Population With Renal Uric Acid Stone

Previous studies suggest that patients with nephrolithiasis exhibit dysbiosis in their gut microbiota, but those studies were conducted in calcium oxalate stone patients. We aimed to explore the association of gut microbiota and biochemical features of renal uric acid stone (UAS) patients in a Chinese population and identify the related bacteria that may affect the pathopoiesis of UAS. A case-control study of 117 patients with UAS, 123 patients with gout, and 135 healthy controls were included from January 2014 to October 2020. For each subject, data on demographics, biochemical parameters of blood and urine were analyzed. Fifteen patients with gout, 16 patients with UAS, 17 UAS patients with gout, and 17 healthy subjects were enrolled and provided fecal samples. The characteristics of gut microbiota were explored by using 16S ribosomal RNA (rRNA) gene sequencing and analyzed by using a combination of software mother and R. Hyperuricemia was the main risk factor for the development of gout and UAS. Obesity, dyslipidemia, and aciduria were unique risk factors for UAS patients. The richness, diversity, and relative abundance of dominant bacteria at the phylum and genus levels of gut microbiota in UAS patients were significantly distinct from other subjects. Abundance of Bacteroides and Fusobacterium was significantly positively correlated with the serum uric acid (UA) level of UAS patients. Fusobacteria was involved in the metabolism and degradation of certain short-chain fatty acids, amino acids, and sugars in pathopoiesis of UAS, and inhibited their synthesis pathways. Fusobacteria may be related to the pathogenesis of UAS, and this finding contributes to the personalized treatment of UAS from the perspective of maintaining micro-ecological equilibrium in gut.

Impact of Different Diets on Adult Tri-Spine Horseshoe Crab, Tachypleus tridentatus

Effective culture and management of adult tri-spine horseshoe crab, Tachypleus tridentatus can ensure that stock enhancement programs and aquaculture systems are maintained. To explore suitable feed for animals during the breeding season, Pacific oyster (Ostrea gigas) (oyster group; OG) and frozen sharpbelly fish (Hemiculter leucisculus) (frozen fish group; FG) were selected to feed 20 T. tridentatus male and female pairs, respectively. At the end of the experiment, intestinal samples were obtained to measure digestive enzymes activities. The intestinal flora were determined by 16S rDNA sequencing. No eggs were observed in the FG and one T. tridentatus adult died. No animals died in the OG, and 9.7 × 10⁴ eggs were obtained. These results show that oysters are more suitable for the development and reproduction of adult T. tridentatus than frozen fish. Additionally, the digestive enzyme activity analysis revealed that animals in the OG exhibited higher protein digestibility than those in the FG, but no significant differences in lipid and carbohydrate uptake were observed between the groups. Furthermore, the intestinal flora analysis showed that operational taxonomic units (OTUs) and the Chao1 index were significantly higher in the OG than in the FG, but no significant difference was observed in the Shannon or Simpson indices between the groups. Our data indicate that the oyster diet improved the intestinal microbial diversity of T. tridentatus. We hypothesize that nutrients, such as oyster-based taurine, proteins, and highly unsaturated fatty acids, improve protease activity in the T. tridentatus digestive tract, alter the intestinal floral structure, and improve the reproductive performance of T. tridentatus.

Changes in the Diversity and Composition of Gut Microbiota of Red-Crowned Cranes (Grus japonensis) after Avian Influenza Vaccine and Anthelmintic Treatment

Gut microbiota homeostasis is important for host health and well-being; however, drugs may affect the composition and function of the gut microbiota. Red-crowned cranes are a vulnerable species. Treatment of red-crowned cranes with avian influenza vaccines and anthelmintics has played pivotal roles in therapeutic management in zoos. To investigate the changes in the diversity and composition of gut microbiota after the avian influenza vaccine and anthelmintic treatment, we used 16S rRNA sequencing to obtain and compare the bacterial community composition before and after the treatment. The alpha diversity of the gut microbiota of red-crowned cranes decreased on the day of the treatment and then fluctuated over time. The composition of gut microbiota tended to be similar in the short term after the treatment, as supported by the beta diversity hierarchical cluster analysis. Only 3, 8, and 72 operational taxonomic units (OTUs) of the three individuals were shared among the five groups before and after treatment. The relative abundance of Firmicutes significantly increased to 99.04% ± 0.28% on the day of the treatment, in which the relative abundance of Lactobacillus was 93.33% ± 5.85%. KEGG pathways analysis indicated that the main function of the gut microbiota is involved in metabolism, and the present study indicates that the gut microbiota of red-crowned cranes is resilient to the avian influenza vaccine and anthelmintic, even disordered in the short term, and could recover over time. More individual experimentation and functional potential in metabolism are needed in the future to support animal disease control and optimal management in the zoo.

Comprehensive Genome-Scale Analysis of Esophageal Carcinoma With Esophageal Tissue-Resident Micro-Environment Discrepancy

To figure out the molecular mechanism in the esophageal squamous carcinoma (ESCC) with the discrepancy in the tissue-resident microbiota, we selected clinical features, RNA sequences, and transcriptomes of ESCC patients from The Cancer Genome Atlas (TCGA) website and detailed tissue-resident microbiota information from The Cancer Microbiome Atlas (n = 60) and explored the infiltration condition of particular microbiota in each sample. We classified the tissue-resident micro-environment of ESCC into two clusters (A and B) and built a predictive classifier model. Cluster A has a higher proportion of certain tissue-resident microbiota with comparatively better survival, while Cluster B has a lower proportion of certain tissue-resident microbiota with comparatively worse survival. We showed traits of gene and clinicopathology in the esophageal tissue-resident micro-environment (ETM) phenotypes. By comparing the two clusters’ molecular signatures, we find that the two clusters have obvious differences in gene expression and mutation, which lead to pathway expression discrepancy. Several pathways are closely related to tumorigenesis. Our results may demonstrate a synthesis of the infiltration pattern of the esophageal tissue-resident micro-environment in ESCC. We reveal the mechanism of esophageal tissue-resident microbiota discrepancy in ESCC, which may contribute to therapy progress for patients with ESCC.

Creutzfeldt-Jakob Disease: Alterations of Gut Microbiota

Introduction

Human gut dysbiosis has been implicated with the onset of many neurodegenerative disorders. However, the current data focused on the gut microbiota of patients with Creutzfeldt-Jakob disease (CJD) are still lacking. In our study, we explored the gut microbiota alteration in patients with CJD.

Method

We performed 16S ribosomal RNA MiSeq sequencing in stool samples of patients with CJD and controls. Functional analysis of the gut microbiota between these two groups was based on Kyoto Encyclopedia of Genes and Genomes and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2. Clinical rating scales were used to evaluate the association between cognitive impairment and gut microbiota alteration.

Result

We identified a significant alteration in both the structure and the richness of the CJD group. Function analysis revealed that the gut microbiota of patients with CJD enriched in immune signaling molecule interactions and xenobiotics biodegradation. MoCA and survival times were found to be associated with gut microbiota in patients with CJD.

Conclusion

We demonstrated an altered gut microbiota in patients with CJD, which was associated with the cognitive impairment and the survival time of these patients.

Gut Bacterial Composition and Functional Potential of Tibetan Pigs Under Semi-Grazing

Gut bacterial community plays a key role in maintaining host health. The Tibetan pig (Sus scrofa), an ancient breed in China, has been known for its high adaptability to harsh environments and for its meat quality. To understand the underlying mechanisms facilitating to shape these unique features, in this study, 16S rRNA sequencing using pigs feces and subsequent bacterial functional prediction were performed. Also, the gut bacteria of two other breeds of pigs, Barkshire and Landrace, were examined for comparison. It was revealed that the structure of bacterial community in Tibetan pigs appeared to be more complex; the relative abundances of dominant bacterial families varied inversely with those of the other pigs, and the proportion of Firmicutes in Tibetan pigs was lower, but Bacteroides, Fibrobacterota, Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae were higher. Bacterial functional prediction revealed that the dominant flora in the Tibetan pigs was more correlated with functions regulating the hosts’ immune and inflammatory responses, such as NOD-like_receptor_signaling_pathway and vitamin metabolism. In addition, in Tibetan pigs, the taxonomic relationships in the gut bacteria on day 350 were closer than those on earlier stages. Furthermore, gender played a role in the composition and function of bacterial inhabitants in the gut; for boars, they were more correlated to drug resistance and xenobiotics metabolism of the host compared to the sows. In sum, our preliminary study on the gut bacterial composition of the Tibetan pigs provided an insight into the underlying host–microorganism interactions, emphasizing the role of intestinal bacteria in the context of modulating the host’s immune system and host development.

KMT2A: Umbrella Gene for Multiple Diseases

KMT2A (Lysine methyltransferase 2A) is a member of the epigenetic machinery, encoding a lysine methyltransferase responsible for the transcriptional activation through lysine 4 of histone 3 (H3K4) methylation. KMT2A has a crucial role in gene expression, thus it is associated to pathological conditions when found mutated. KMT2A germinal mutations are associated to Wiedemann–Steiner syndrome and also in patients with initial clinical diagnosis of several other chromatinopathies (i.e., Coffin–Siris syndromes, Kabuki syndrome, Cornelia De Lange syndrome, Rubinstein–Taybi syndrome), sharing an overlapping phenotype. On the other hand, KMT2A somatic mutations have been reported in several tumors, mainly blood malignancies. Due to its evolutionary conservation, the role of KMT2A in embryonic development, hematopoiesis and neurodevelopment has been explored in different animal models, and in recent decades, epigenetic treatments for disorders linked to KMT2A dysfunction have been extensively investigated. To note, pharmaceutical compounds acting on tumors characterized by KMT2A mutations have been formulated, and even nutritional interventions for chromatinopathies have become the object of study due to the role of microbiota in epigenetic regulation.

Effect of Changes in Photoperiods on Melatonin Expression and Gut Health Parameters in Laying Ducks

We investigated the effect of photoperiod on ileal morphology, barrier function, short-chain fatty acid (SCFA) contents, microbial flora, melatonin expression, and synthesis in laying ducks. After adaption, a total of 180 Jinding laying ducks (252 days old) were randomly divided into three treatments, receiving 12L (hours of light):12D (hours of darkness), 16L:8D, or 20L:4D. Each treatment had six replicates with 10 birds each. The formal experiment lasted 58 days. Compared with 12L:12D, the significantly higher values of villus height and goblet cell percentage (GCP) were observed in 16L:8D treatment, accompanied with the higher mRNA relative expression of zonula occludens-1, zonula occludens-2, zonula occludens-3, claudin-1, occludin, and mucin 2 (P < 0.05). Besides, significantly higher values of acetate and propionate, butyrate and total SCFA concentrations were simultaneously observed in ileal chyme of 16L:8D treatment (P < 0.05). For the ileal microbial community, the results of principal coordinate analysis (PCoA) visually presented that three photoperiod groups were mainly scattered into three clusters, indicating that the microbiota composition in different photoperiod treatments were quite dissimilar. Lower values of Shannon indicators were observed in the 20L:4D treatment (P < 0.05), meaning that the microbiota α-diversity decreased in the 20-h photoperiod. The relative abundance of Actinobacteria, Fusobacteria, and Proteobacteria at phylum level and Fusobacterium, Clostridium_sensu_stricto_1, and Pectobacterium at genus level kept an appropriate balance in the 16L:8D photoperiod. Melatonin level in serum decreased with the increasing photoperiods at 6:00 and 12:00, which was consistent with melatonin receptor expressions in the hypothalamus and ileal tissue. Meanwhile, the adenosine 3′,5′-cyclic phosphate (cAMP) contents were significantly downregulated in the pineal gland (P < 0.05), in response to the increase in photoperiod. In conclusion, an appropriate photoperiod could improve ileal morphology, barrier function, SCFA profile, and microbial flora, which may be attributed to the appropriate regulation of the circadian rhythm through melatonin as well as its receptor expression, and 16 h could be an adequate photoperiod for laying ducks.

Dysbiosis of skin microbiome and gut microbiome in melanoma progression

Background

The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression.

Results

Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier.

Conclusion

The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02458-5.

Characterization of Bacterial Microbiota Composition in Healthy and Diarrheal Early-Weaned Tibetan Piglets

The occurrence of diarrhea in Tibetan piglets is highly notable, but the microorganisms responsible are yet unclear. Its high incidence results in serious economic losses for the Tibetan pig industry. Moreover, the dynamic balance of intestinal microflora plays a crucial role in maintaining host health, as it is a prime cause of diarrhea. Therefore, the present study was performed to analyze the characteristics of bacterial microbiota structure in healthy, diarrheal and treated weaned piglets in Tibet autonomous region for providing a theoretical basis to prevent and control diarrhea. The study was based on the V3–V4 region of the 16S rRNA gene and gut microbiota functions following the metagenome analysis of fresh fecal samples (n = 5) from different groups. The Shannon and Simpson indices differed substantially between diarrheal and treated groups (p < 0.05). According to our findings, the beta diversities, especially between healthy and diarrheal groups, were found different. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla in three groups. Furthermore, the abundance of Fusobacteria in the diarrheal group was higher than the other groups. The dominant genera in the diarrheal group were Fusobacterium, Butyricimonas, Sutterella, Peptostreptococcus, and Pasteurella. Moreover, Lactobacillus, Megasphaera and Clavibacter were distinctly less abundant in this group. It is noteworthy that the specific decrease in the abundance of pathogenic bacteria after antibiotic treatment in piglets was noticed, while the level of Lactobacillus was evidently increased. In conclusion, fecal microbial composition and structure variations were discovered across the three groups. Also, the ecological balance of the intestinal microflora was disrupted in diarrheal piglets. It might be caused by a reduction in the relative number of beneficial bacteria and an increase in the abundance of pathogenic bacteria. In the context of advocating for non-resistant feeding, we suspect that the addition of probiotics to feed may prevent early-weaning diarrhea in piglets. Moreover, our findings might help for preventing diarrhea in weaned Tibetan piglets with a better understanding of microbial population dynamics.

The Association of Microbiome Dysbiosis With Colorectal Cancer

Many studies have been conducted to identify the causative organisms in colorectal cancer (CRC) and compare the microbiota of healthy individuals and those with CRC. The pathways by which the microbiota promotes CRC development are not yet fully understood. The hypothesized mechanisms include damage to the DNA, production of carcinogenic metabolites, and promotion of chronic inflammation. In a state of dysbiosis, the gut loses protective bacteria and is enriched with pathogenic and cancer-promoting bacteria, which promotes functions associated with cancer such as angiogenesis, loss of apoptosis, and cell proliferation. We have established a strong link between microbiota dysbiosis and certain species of bacteria and even viruses involved in tumorigenesis. In this review, we look at some of the major identified species and how they are related to CRC. Future research should include and even focus on mycobiome and virome on CRC development. Due to the diversity of the gut microbiome, there is a high possibility that the gain and loss of bacteria and their metabolic functions lead to CRC.

Ammonia stress disrupts intestinal microbial community and amino acid metabolism of juvenile yellow catfish (Pelteobagrus fulvidraco)

Ammonia has adverse effects on aquatic animals, which is also widely distributed in natural aquatic environments and intensive aquaculture systems. The intestine is a primary defensive line for aquatic animals, the accumulation of ammonia in the aquatic environment can cause irreversible damage to intestinal function. In this study, we investigated the effects of acute ammonia stress on the reaction characteristics of digestive function, amino acid metabolism, and the variation in the intestinal microbiota of juvenile yellow catfish (Pelteobagrus fulvidraco). Thus, the yellow catfish was placed in water with the addition of ammonia at 0 (control), 14.6, and 146 mg/L total ammonia nitrogen for 96-h. The present study observed that ammonia accumulated in the intestine and muscle (ammonia contents in the intestine and muscle increased) and induced the activities of protein digestive enzymes dysfunction (pepsin increased while trypsin decreased). Ammonia stress changed various amino acids composition (proline, arginine, lysine, histidine, phenylalanine, tyrosine, leucine, isoleucine, valine, alanine, glutamic acid, tyrosine, and aspartic acid contents were increased in muscle) and increased the activities of alanine aminotransferase and aspartate aminotransferase in muscle. Furthermore, through 16 S rRNA gene analysis, ammonia stress-induced reduction in diversity, richness, and evenness and structure of microbiota alteration in the intestine. At the phylum level, the abundance of Fusobacteria increased while Firmicutes and Actinobacteria decreased significantly. At the genus level, the abundance of beneficial microbiota Cetobacterium significantly increased after ammonia stress. In conclusion, activation of amino acid synthesis in muscle may be involved in ammonia detoxification after severe ammonia stress. The accumulation of ammonia can disrupt the intestinal digestive function and intestinal microbiota community. The Cetobacterium may be a new potential positive factor in the resistance of ammonia toxicity.

Effects of Dietary Glucose Oxidase Supplementation on the Performance, Apparent Ileal Amino Acids Digestibility, and Ileal Microbiota of Broiler Chickens

Simple Summary

Glucose oxidase was used as a potential additive to improve intestinal health in livestock and poultry industry. This study aimed to investigate the effects of glucose oxidase supplementation on performance, ileal microbiota, ileal short-chain fatty acids profile, and apparent ileal digestibility in grower broilers. Our findings will provide a valuable insight into the possibility of glucose oxidase as an alternative of antibiotic growth promoters in broiler diets.

Abstract

This study aimed to investigate the effects of glucose oxidase (GOD) supplementation on growth performance, apparent ileal digestibility (AID) of nutrients, intestinal morphology, and short-chain fatty acids (SCFAs) and microbiota in the ileum of broilers. Six hundred 1-day-old male broilers were randomly allotted to four groups of 10 replicates each with 15 birds per replicate cage. The four treatments included the basal diet without antibiotics (Control) and the basal diet supplemented with 250, 500, or 1000 U GOD/kg diet (E250, E500 or E1000). The samples of different intestinal segments, ileal mucosa, and ileal digesta were collected on d 42. Dietary GOD supplementation did not affect daily bodyweight gain (DBWG) and the ratio of feed consumption and bodyweight gain (FCR) during d 1-21 (p > 0.05); however, the E250 treatment increased DBWG (p = 0.03) during d 22–42 as compared to control. Dietary GOD supplementation increased the AIDs of arginine, isoleucine, lysine, methionine, threonine, cysteine, serine, and tyrosine (p < 0.05), while no significant difference was observed among the GOD added groups. The E250 treatment increased the villus height of the jejunum and ileum. The concentrations of secreted immunoglobulin A (sIgA) in ileal mucosa and the contents of acetic acid and butyric acid in ileal digesta were higher in the E250 group than in the control (p < 0.05), whereas no significant differences among E500, E1000, and control groups. The E250 treatment increased the richness of ileal microbiota, but E500 and E100 treatment did not significantly affect it. Dietary E250 treatment increased the relative abundance of Firmicutes phylum and Lactobacillus genus, while it decreased the relative abundance of genus Escherichina-Shigella (p < 0.05). Phylum Fusobacteria only colonized in the ileal digesta of E500 treated broilers and E500 and E1000 did not affect the relative abundance of Firmicutes phylum and Lactobacillus and Escherichina-Shigella genera as compared to control. These results suggested that dietary supplementation of 250 U GOD/kg diet improves the growth performance of broilers during d 22–42, which might be associated with the alteration of the intestinal morphology, SCFAs composition, and ileal microbiota composition.

Dietary Valine Ameliorated Gut Health and Accelerated the Development of Nonalcoholic Fatty Liver Disease of Laying Hens

Valine is an important essential amino acid of laying hens. Dietary supplemented with BCAAs ameliorated gut microbiota, whereas elevated blood levels of BCAAs are positively associated with obesity, insulin resistance, and diabetes in both humans and rodents. General controlled nonrepressed (GCN2) kinase plays a crucial role in regulating intestinal inflammation and hepatic fatty acid homeostasis during amino acids deficiency, while GCN2 deficient results in enhanced intestinal inflammation and developed hepatic steatosis. However, how long-term dietary valine impacts gut health and the development of nonalcoholic fatty liver disease (NAFLD) remains unknown. Hence, in the present study, we elucidated the effects of dietary valine on intestinal barrier function, microbial homeostasis, and the development of NAFLD. A total of 960 healthy 33-weeks-old laying hens were randomly divided into five experimental groups and fed with valine at the following different levels in a feeding trial that lasted 8 weeks: 0.59, 0.64, 0.69, 0.74, and 0.79%, respectively. After 8 weeks of treatment, related tissues and cecal contents were obtained for further analysis. The results showed that diet supplemented with valine ameliorated gut health by improving intestinal villus morphology, enhancing intestinal barrier, decreasing cecum pathogenic bacteria abundances such as Fusobacteriota and Deferribacterota, and inhibiting inflammatory response mediated by GCN2. However, long-term intake of high levels of dietary valine (0.74 and 0.79%) accelerated the development of NAFLD of laying hens by promoting lipogenesis and inhibiting fatty acid oxidation mediated by GCN2-eIF2α-ATF4. Furthermore, NAFLD induced by high levels of dietary valine (0.74 and 0.79%) resulted in strengthening oxidative stress, ER stress, and inflammatory response. Our results revealed that high levels of valine are a key regulator of gut health and the adverse metabolic response to NAFLD and suggested reducing dietary valine as a new approach to preventing NAFLD of laying hens.

The gut microbiome in sickle cell disease: Characterization and potential implications

BACKGROUND

Sickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized deoxygenated hemoglobin, rigid sickle red blood cells and vaso-occlusive crises (VOC). Recurrent hypoxia-reperfusion injury in the gut of SCD patients could increase tissue injury, permeability, and bacterial translocation. In this context, the gut microbiome, a major player in health and disease, might have significant impact. This study sought to characterize the gut microbiome in SCD.

METHODS

Stool and saliva samples were collected from healthy controls (n = 14) and SCD subjects (n = 14). Stool samples were also collected from humanized SCD murine models including Berk, Townes and corresponding control mice. Amplified 16S rDNA was used for bacterial composition analysis using Next Generation Sequencing (NGS). Pairwise group analyses established differential bacterial groups at many taxonomy levels. Bacterial group abundance and differentials were established using DeSeq software.

RESULTS

A major dysbiosis was observed in SCD patients. The Firmicutes/Bacteroidetes ratio was lower in these patients. The following bacterial families were more abundant in SCD patients: Acetobacteraceae, Acidaminococcaceae, Candidatus Saccharibacteria, Peptostreptococcaceae, Bifidobacteriaceae, Veillonellaceae, Actinomycetaceae, Clostridiales, Bacteroidacbactereae and Fusobacteriaceae. This dysbiosis translated into 420 different operational taxonomic units (OTUs). Townes SCD mice also displayed gut microbiome dysbiosis as seen in human SCD.

CONCLUSION

A major dysbiosis was observed in SCD patients for bacteria that are known strong pro-inflammatory triggers. The Townes mouse showed dysbiosis as well and might serve as a good model to study gut microbiome modulation and its impact on SCD pathophysiology.

Effects of Dietary Macronutrient Profile on Apparent Total Tract Macronutrient Digestibility and Fecal Microbiota, Fermentative Metabolites, and Bile Acids of Female Dogs after Spay Surgery

Obesity and estrogen reduction are known to impact the gut microbiota and gut microbial-derived metabolites in some species, but limited information is available in dogs. The aim of this study was to determine the effects of dietary macronutrient profile on apparent total tract macronutrient digestibility, fecal microbiota, and fecal metabolites of adult female dogs after spay surgery. Twenty-eight adult intact female beagles (age: 3.02 ± 0.71 yr, BW: 10.28 ± 0.77 kg; BCS: 4.98 ± 0.57) were used. After a 5-wk baseline phase (wk 0), 24 dogs were spayed and randomly allotted to one of three experimental diets (n=8/group): 1) control (CO) containing moderate protein and fiber (COSP), 2) high-protein, high-fiber (HPHF), or 3) high-protein, high-fiber plus omega-3 and medium-chain fatty acids (HPHFO). Four dogs were sham-operated and fed CO (COSH). All dogs were fed to maintain BW for 12 wk after spay, then allowed to consume twice that amount for 12 wk. Fecal samples were collected at wk 0, 12, and 24 for digestibility, microbiota, and metabolite analysis. All data were analyzed using repeated measures and linear Mixed Models procedure of SAS 9.4, with results reported as change from baseline. Apparent organic matter and energy digestibilities had greater decreases in HPHF and HPHFO than COSH and COSP. Increases in fecal acetate, total short-chain fatty acids, and secondary bile acids were greater and decreases in primary bile acids were greater in HPHF and HPHFO. Principal coordinates analysis of weighted UniFrac distances revealed that HPHF and HPHFO clustered together and separately from COSH and COSP at wk 12 and 24, with relative abundances of Faecalibacterium, Romboutsia, and Fusobacterium increasing to a greater extent and Catenibacterium, Bifidobacterium, Prevotella 9, Eubacterium, and Megamonas decreasing to a greater extent in HPHF or HPHFO. Our results suggest that high-protein, high-fiber diets alter nutrient and energy digestibilities, fecal metabolite concentrations, and fecal gut microbiota, but spay surgery had minor effects. Future research is needed to investigate how food intake, nutrient profile, and changes in hormone production influence gut microbiota and metabolites of dogs individually and how this knowledge may be used to manage spayed pets.

Characteristics of the bacterial microbiota in the upper respiratory tract of children

PURPOSE

The respiratory tract microbiota are deemed as the gatekeeper to health. Consequently, microbiota dysbiosis can lead to the development of diseases. To identify the exact origins of the localized pathogenic bacteria, we investigated bacterial composition in the upper airway tract.

METHODS

Separate mucosal swabs were collected from nostril or oropharynx of each participant. Meanwhile, the lymphoid tissues including adenoids and tonsils were collected during operation. DNAs were exacted from all the samples for the following 16S rRNA analysis.

RESULTS

At the phylum level, the basic bacterial structures in the adenoids, tonsils, oropharynx, and nostrils were generally similar: five main phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria form the majority of the microbiota. However, across these four sites, the microbiota composition differed. More specifically, the bacterial composition in the nostrils was unique. There, Firmicutes and Actinobacteria were the most abundant phyla, while Bacteroides and Fusobacteria were the least abundant. At the genus level, Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella were the most plentiful, while Fusobacteria was the least ample. Across all sites, Streptococcus displayed similar abundances. Fusobacteria exhibited higher abundances in the lymphoid tissues and oropharynx. Haemophilus and Neisseria were more plentiful in the tonsils and oropharynx. Notably, Klebsiella, which is normally localized to the gut, was abundant in the adenoids and tonsils.

CONCLUSION

Our data indicate that promising pathogenic bacteria originate from all sites in the upper airway. The upper tract lymphoid tissues, normally considered as immune organs, may also serve as reservoirs for pathogenic bacteria.

A Crosstalk between Diet, Microbiome and microRNA in Epigenetic Regulation of Colorectal Cancer

A still growing interest between human nutrition in relation to health and disease states can be observed. Dietary components shape the composition of microbiota colonizing our gastrointestinal tract which play a vital role in maintaining human health. There is a strong evidence that diet, gut microbiota and their metabolites significantly influence our epigenome, particularly through the modulation of microRNAs. These group of small non-coding RNAs maintain cellular homeostasis, however any changes leading to impaired expression of miRNAs contribute to the development of different pathologies, including neoplastic diseases. Imbalance of intestinal microbiota due to diet is primary associated with the development of colorectal cancer as well as other types of cancers. In the present work we summarize current knowledge with particular emphasis on diet-microbiota-miRNAs axis and its relation to the development of colorectal cancer.

Effects of Bacillus amyloliquefaciens Instead of Antibiotics on Growth Performance, Intestinal Health, and Intestinal Microbiota of Broilers

The aim of this study was to evaluate the dietary effects of Bacillus amyloliquefaciens SC06 (SC06) instead of antibiotics on the growth performance, intestinal health, and intestinal microbiota of broilers. A total of 360 30-day-old Lingnan yellow broilers were randomly allocated into two groups with six replicates per group (30 birds per replicate). The broilers were fed either a non-supplemented diet or a diet supplemented with 10⁸ colony-forming units lyophilized SC06 per kilogram feed for 30 days. Results showed that SC06 supplementation had no effect on the growth performance compared with that of the control group. SC06 treatment significantly (P <0.05) increased the total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) activity in the liver, and the activities of trypsin, α-amylase (AMS), and Na⁺K⁺-ATPase in the ileum, whereas it decreased (P < 0.05) lipase, gamma glutamyl transpeptidase (γ-GT), and maltase activities in the ileum. Meanwhile, SC06 treatment also improved the immune function indicated by the significantly (P < 0.05) increased anti-inflammatory cytokine [interleukin (IL)-10] level and the decreased (P < 0.05) pro-inflammatory cytokine [IL-6 and tumor necrosis factor (TNF)-α] levels in the ileum. Furthermore, we also found that SC06 enhanced the intestinal epithelial intercellular integrity (tight junction and adhesion belt) in the ileum. Microbial analysis showed that SC06 mainly increased the alpha diversity indices in the jejunum, ileum, and cecum. SC06 treatment also significantly (P < 0.05) increased the abundances of Bacteroidetes, Bacteroidales, Bacteroides, Fusobacteria, Clostridiaceae, and Veillonellaceae in the cecum and simultaneously decreased the abundances of Planococcaceae in the duodenum, Microbacteriaceae in the jejunum, and Lachnospiraceae, [Ruminococcus] and Ruminococcus in cecum. In conclusion, these results suggested that B. amyloliquefaciens instead of antibiotics showed a potential beneficial effect on the intestinal health of broilers.

Shifts in the Oral Microbiota During a Four-Week Commercial Saturation Dive to 200 Meters

During commercial saturation diving, divers live and work under hyperbaric and hyperoxic conditions. The myriads of bacteria that live in and on the human body must adjust to the resultant hyperbaric stress. In this study, we examined the shifts in bacterial content in the oral cavity of saturation divers, using a metagenomic approach to determine the diversity in the composition of bacterial phyla and genera in saliva from 23 male divers before, during, and immediately after 4 weeks of commercial heliox saturation diving to a working depth of circa 200 m. We found that the bacterial diversity fell during saturation, and there was a change in bacterial composition; with a decrease at the phylum level of obligate anaerobe Fusobacteria, and an increase of the relative abundance of Actinobacteria and Proteobacteria. At the genus level, Fusobacterium, Leptotrichia, Oribacterium, and Veillonella decreased, whereas Neisseria and Rothia increased. However, at the end of the decompression, both the diversity and composition of the microbiota returned to pre-dive values. The results indicate that the hyperoxic conditions during saturation may suppress the activity of anaerobes, leaving a niche for other bacteria to fill. The transient nature of the change could imply that hyperbaric heliox saturation has no lasting effect on the oral microbiota, but it is unknown whether or how a shift in oral bacterial diversity and abundance during saturation might impact the divers’ health or well-being.

The dysbiosis signature of Fusobacterium nucleatum in colorectal cancer-cause or consequences? A systematic review

Colorectal cancer (CRC) is the third most common cause of cancer globally and the fourth attributable cause of mortality and morbidity due to cancer. An emerging factor contributing to CRC is the gut microbiota and the cellular changes associated with it. Further insights on this may help in the prevention, diagnosis and new therapeutic approaches to colorectal cancer. In most cases of CRC, genetic factors appear to contribute less to its aetiology than environmental and epigenetic factors; therefore, it may be important to investigate these environmental factors, their effects, and the mechanisms that may contribute to this cancer. The gut microbiota has recently been highlighted as a potential risk factor that may affect the structural components of the tumor microenvironment, as well as free radical and enzymatic metabolites directly, or indirectly. Many studies have reported changes in the gut microbiota of patients with colorectal cancer. What is controversial is whether the cancer is the cause or consequence of the change in the microbiota. There is strong evidence supporting both possibilities. The presence of Fusobacterium nucleatum in human colorectal specimens has been demonstrated by RNA-sequencing. F. nucleatum has been shown to express high levels of virulence factors such as FadA, Fap2 and MORN2 proteins. Our review of the published data suggest that F. nucleatum may be a prognostic biomarker of CRC risk, and hence raises the potential of antibiotic treatment of F. nucleatum for the prevention of CRC.

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life

Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.

Effects of manganese and Bacillus subtilis on the reproductive performance, egg quality, antioxidant capacity, and gut microbiota of breeding geese during laying period

This experiment was conducted to investigate the effects of manganese (Mn) and Bacillus subtilis (BS) on the production performance, egg quality, antioxidant capacity, and gut microbiota of breeding geese during laying period. A total of 120 forty-six-week-old breeding geese (Wulong) were randomly assigned to 1 of 6 treatment diets formulated to supply 10, 20, and 30 mg/kg Mn with 5 × 109 CFU/kg or 2.5 × 109 CFU/kg BS for a 10-wk trial. Results showed that dietary supplementation with 20 and 30 mg/kg Mn could decrease the daily feed intake (DFI) of geese. Moreover, 30 mg/kg Mn significantly increased the laying rate. Besides, although Mn addition had no obvious effect on egg quality, 5 × 109 CFU/kg BS was found to elevate the hatching egg hatching rate and eggshell thickness. For the serum hormones, 30 mg/kg Mn promoted estradiol secretion, while 5 × 109 CFU/kg BS increased the level of follicle-stimulating hormone. Furthermore, 20 and 30 mg/kg Mn and 5 × 109 CFU/kg BS significantly enhanced the total antioxidant capacity by increasing the activity of total superoxide dismutases or decreasing the content of malondialdehyde. Dietary supplementation with 5 × 109 CFU/kg BS also increased the intestinal villus height and upregulated the abundance of Fusobacteria, Fusobacteriaceae, Fusobacterium, and Faecalibacterium in cecal content. In addition, 20 and 30 mg/kg Mn elevated the levels of Bacteroidetes, Bacteroidaceae, Bacteroides, and Ruminococcaceae but decreased Streptococcaceae. Importantly, an interaction effect was observed between Mn and BS on the DFI, egg mass, average egg size, and the abundance of Bacteroides as well as Faecalibacterium. In conclusion, dietary inclusion of Mn and BS could improve the production performance, egg quality, antioxidant capacity, intestinal structure, as well as gut microbiota. Supplementation of 30 mg/kg Mn and 5.0 × 109 CFU/kg BS provided the optimal effect.

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet

Background

The fecal microbiota from obese individuals can induce obesity in animal models. In addition, studies in humans, animal models and dogs have revealed that the fecal microbiota of subjects with obesity is different from that of lean subjects and changes after weight loss. However, the impact of weight loss on the fecal microbiota in dogs with obesity has not been fully characterized.

Methods

In this study, we used 16S rRNA gene sequencing to investigate the differences in the fecal microbiota of 20 pet dogs with obesity that underwent a weight loss program. The endpoint of the weight loss program was individually tailored to the ideal body weight of each dog. In addition, we evaluated the qPCR based Dysbiosis Index before and after weight loss.

Results

After weight loss, the fecal microbiota structure of dogs with obesity changed significantly (_weightedANOSIM; p = 0.016, R = 0.073), showing an increase in bacterial richness (p = 0.007), evenness (p = 0.007) and the number of bacterial species (p = 0.007). The fecal microbiota composition of obese dogs after weight loss was characterized by a decrease in Firmicutes (92.3% to 78.2%, q = 0.001), and increase in Bacteroidetes (1.4% to 10.1%, q = 0.002) and Fusobacteria (1.6% to 6.2%, q = 0.040). The qPCR results revealed an overall decrease in the Dysbiosis Index, driven mostly due to a significant decrease in E. coli (p = 0.030), and increase in Fusobacterium spp. (p = 0.017).

Conclusion

The changes observed in the fecal microbiota of dogs with obesity after weight loss with a weight loss diet rich in fiber and protein were in agreement with previous studies in humans, that reported an increase of bacterial biodiversity and a decrease of the ratio Firmicutes/Bacteroidetes.