Colonic Bacterial Composition Research Articles

Corrigendum: A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis

Corrigendum: A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation

BackgroundIn the pig production, diarrhea can occur during different growth stages including the period 4–16 weeks post weaning, during which a diarrheal outbreak also termed as colitis-complex diarrhea (CCD) can occur and it is distinct from post-weaning diarrhea (1–2 weeks post weaning). We hypothesized that CCD in growing pigs is associated with changes in colonic microbiota composition and fermentation patterns, and the aim of the present observational study was to identify changes in digesta-associated bacteria (DAB) and mucus-associated bacteria (MAB) in the colon of growing pigs with and without diarrhea. A total number of 30 pigs (8, 11, and 12 weeks of age) were selected; 20 showed clinical signs of diarrhea and 10 appeared healthy. Based on histopathological examination of colonic tissues, 21 pigs were selected for further studies and classified as follows: without diarrhea, no colon inflammation (NoDiar; n = 5), with diarrhea, without colonic inflammation (DiarNoInfl; n = 4), and with diarrhea, with colonic inflammation (DiarInfl; n = 12). Composition (based on 16S rRNA gene amplicon sequencing) and fermentation pattern (short-chain fatty acids; SCFA profile) of the DAB and MAB communities were characterized.ResultsThe DAB showed higher alpha diversity compared to MAB in all pigs, and both DAB and MAB showed lowest alpha diversity in the DiarNoInfl group. Beta diversity was significantly different between DAB and MAB as well as between diarrheal groups in both DAB and MAB. Compared to NoDiar, DiarInfl showed increased abundance of various taxa, incl. certain pathogens, in both digesta and mucus, as well as decreased digesta butyrate concentration. However, DiarNoInfl showed reduced abundance of different genera (mainly Firmicutes) compared to NoDiar, but still lower butyrate concentration.ConclusionDiversity and composition of MAB and DAB changed in diarrheal groups depending on presence/absence of colonic inflammation. We also suggest that DiarNoInfl group was at the earlier stage of diarrhea compared with DiarInfl, with a link to dysbiosis of colonic bacterial composition as well as reduced butyrate concentration, which plays a pivotal role in gut health. This could have led to diarrhea with inflammation due to a dysbiosis, associated with an increase in e.g., Escherichia-Shigella (Proteobacteria), Helicobacter (Campylobacterota), and Bifidobacterium (Actinobacteriota), which may tolerate or utilize oxygen and cause epithelial hypoxia and inflammation. The increased consumption of oxygen in epithelial mucosal layer by infiltrated neutrophils may also have added up to this hypoxia. Overall, the results confirmed that changes in DAB and MAB were associated with CCD and reduced butyrate concentration in digesta. Moreover, DAB might suffice for future community-based studies of CCD.

Alteration of Colonic Bacterial and Fungal Composition and Their Inter- and Intra-Kingdom Interaction in Patients with Adenomas with Low-Grade Dysplasia.

Colorectal cancer (CRC) develops from pre-cancerous cellular lesions in the gut epithelium and mainly originates from specific types of colonic adenomas with dysplasia. However, gut microbiota signatures among sampling sites in patients with colorectal adenomas with low-grade dysplasia (ALGD) and normal control (NC) remain uncharacterized. To characterize gut microbial and fungal profiles in ALGD and normal colorectal mucosa tissues. We used 16S and ITS1-2 rRNA gene sequencing and bioinformatics analysis on the microbiota of ALGD and normal colorectal mucosa from 40 subjects. Bacterial sequences in the ALGD group showed an increase in Rhodobacterales, Thermales, Thermaceae, Rhodobacteraceae, and several genera, including Thermus, Paracoccus, Sphingobium, and Pseudomonas, compared to the NC group. Fungal sequences in the ALGD group showed an increase in Helotiales, Leotiomycetes, and Basidiomycota, while several orders, families, and genera, including Verrucariales, Russulales, and Trichosporonales, were decreased. The study found various interactions between intestinal bacteria and fungi. The bacterial functional analysis showed increased glycogen and vanillin degradation pathways in the ALGD group. Meanwhile, the fungal functional analysis showed a decrease in pathways related to the biosynthesis of gondoate and stearate, as well as degradation of glucose, starch, glycogen, sucrose, L-tryptophan, and pantothenate, and an increase in the octane oxidation pathway in the ALGD group. The mucosal microbiota in ALGD exhibits altered fungal and microbial composition compared to the NC mucosa, potentially contributing to the development of intestinal cancer by regulating specific metabolic pathways. Therefore, these changes in microbiota and metabolic pathways may be potential markers for diagnosing and treating colorectal adenoma and carcinoma.

A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis.

Ulcerative colitis (UC) is characterized by chronic inflammation in the colonic epithelium and has a blurred etiology. A western diet and microbial dysbiosis in the colon were reported to play a role in UC development. In this study, we investigated the effect of a westernized diet, i.e., increasing fat and protein content by including ground beef, on the colonic bacterial composition in a dextran sulfate sodium (DexSS) challenged pig study. The experiment was carried out in three complete blocks following a 2×2 factorial design including 24 six-week old pigs, fed either a standard diet (CT) or the standard diet substituted with 15% ground beef to simulate a typical westernized diet (WD). Colitis was induced in half of the pigs on each dietary treatment by oral administration of DexSS (DSS and WD+DSS, respectively). Samples from proximal and distal colon and feces were collected. Bacterial alpha diversity was unaffected by experimental block, and sample type. In proximal colon, WD group had similar alpha diversity to CT group and the WD+DSS group showed the lowest alpha diversity compared to the other treatment groups. There was a significant interaction between western diet and DexSS for beta diversity, based on Bray-Curtis dissimilarly. The westernized diet and DexSS resulted in three and seven differentially abundant phyla, 21 and 65 species, respectively, mainly associated with the Firmicutes and Bacteroidota phyla followed by Spirochaetota, Desulfobacterota, and Proteobacteria. The concentration of short-chain fatty acids (SCFA) was lowest in the distal colon. Treatment had a slight effect on the estimates for microbial metabolites that might have valuable biological relevance for future studies. The concentration of putrescine in the colon and feces and that of total biogenic amines was highest in the WD+DSS group. We conclude that a westernized diet could be a potential risk factor and an exacerbating agent for UC by reducing the abundance of SCFA-producing bacteria, increasing the abundance of pathogens such as Helicobacter trogontum, and by increasing the concentration of microbial proteolytic-derived metabolites in the colon.

Effects of dietary protein content and crystalline amino acid supplementation patterns in low protein diets on intestinal bacteria and their metabolites in weaned pigs raised under Different sanitary conditions.

The objective of this experiment was to investigate the effects of dietary crude protein (CP) content and crystalline amino acids (CAA) supplementation patterns in low CP (LCP) diets on intestinal bacteria and their metabolites in weaned pigs raised under clean (CSC) or unclean sanitary conditions (USC). One hundred forty-four piglets (6.35 ± 0.63 kg) were assigned to one of six treatments in a 3 × 2 factorial arrangement based on CP content and sanitary conditions in a randomized complete block design to give eight replicates with three pigs per pen over a 21-d period. Diets consisted of a high CP (HCP; 21%) and two LCP (18%) diets supplemented with 9 CAA (Lys, Met, Thr, Trp, Val, Ile, Leu, His, and Phe) or only six CAA (Lys, Met, Thr, Trp, Val, and Ile) to meet the requirements. The CSC room was washed weekly, whereas the USC room had sow manure spread in the pens from the beginning of the study and was not washed throughout the experiment. Jejunum and colon digesta were sampled on day 21. Both jejunum and colon digesta were analyzed for ammonia nitrogen, short-chain fatty acids, and biogenic amines but only colon digesta was analyzed for microbiome composition (16s rRNA sequencing on MiSeq). Data were analyzed using R software for 16S rRNA and the MIXED procedure of SAS for microbial metabolites. Sanitation, CP content, and CAA supplementation patterns did not affect the diversity of colonic bacterial composition in weaned pigs. Pigs raised under USC had greater (P < 0.05) jejunal ammonia nitrogen concentration than those raised under CSC. Pigs fed LCP diets had reduced (P < 0.05) jejunal ammonia nitrogen concentration compared to those fed the HCP diet. Interactions between sanitation and dietary CP content were observed (P < 0.05) for: (1) jejunal acetate and (2) colonic spermidine and spermine, whereby (1) acetate concentrations decreased from NCP to LCP in pigs raised under the CSC but those concentrations increased under the USC, and (2) spermidine and spermine concentrations increased in LCP diets compared to HCP diet under USC, unlike CSC which did not show any difference between HCP and LCP. In conclusion, reducing dietary CP lowered ammonia nitrogen content regardless of sanitation and increased microbial metabolites in weaned pigs raised under USC. However, LCP diets with different CAA supplementation patterns did not affect bacterial diversity in weaned pigs, regardless of the hygienic conditions where the animals were housed.

PSX-A-4 Effects of Dietary Protein Content and Crystalline Amino Acid Supplementation Patterns on Intestinal Bacteria and Their Metabolites in Weaned Pigs Raised Under Different Sanitary Conditions

Abstract The objective of this experiment was to investigate the effects of dietary crude protein (CP) content and crystalline amino acids (CAA) supplementation patterns on the bacteria and their metabolites in the intestine of weaned pigs raised under clean (CSC) or unclean sanitary conditions (USC). One hundred forty-four piglets (6.35 ± 0.63 kg BW) were assigned to 1 of 3 diets to give 8 replicates, each with 3 pigs, over a 21-days period. Diets consisted of a high CP (HCP; 21%) and two low CP (LCP; 18%) diets supplemented with all 10 essential AA as CAA or only 6 CAA (Lys, Met, Thr, Trp, Val, and Ile). The CSC room was washed weekly, whereas the USC room had sow manure spread in the pens and was not washed throughout the experiment. Digesta from jejunum and colon were analyzed for ammonia N, short-chain fatty acids, and biogenic amines, but only colonic digesta was analyzed for microbiome composition (16s rRNA sequencing on MiSeq). Data were analyzed using R software for 16S rRNA and the MIXED procedure of SAS for microbial metabolites. Sanitation, CP content, and CAA supplementation patterns did not affect colonic bacterial composition or diversity in weaned pigs. Pigs raised under USC had greater (P &amp;lt; 0.05) jejunal ammonia N than those under CSC. Pigs fed LCP diets had reduced (P &amp;lt; 0.05) jejunal ammonia N compared to those fed HCP diet. No difference was found in colonic ammonia N. Interactions between sanitation and dietary CP content were observed (P &amp;lt; 0.05) for jejunal acetate and colonic spermidine and spermine. In conclusion, reducing dietary CP lowered ammonia N content regardless of the sanitation and increased microbial metabolites in weaned pigs raised under USC. However, colonic bacterial composition and diversity were not influenced by dietary CP, sanitary conditions, or CAA supplementation patterns.

Gut Microbiota Alter Visceral Pain Sensation and Inflammation via Modulation of Synthesis of Resolvin D1 in Colonic Tuft Cells.

Background and AimsVisceral hypersensitivity and low grade mucosal inflammation are frequently observed in a subpopulation of irritable bowel syndrome (IBS) patients. The responsible mechanism is unclear. Resolvins are a novel class of anti-inflammatory lipid mediators that regulate resolution of inflammation and pain. We hypothesize that resolvin D1 (RvD1) synthesis is reduced in IBS-D colonic mucosa and contribute to the development of visceral hypersensitivity. MethodsWe used ELISA and qPCR to quantify the levels of RvD1 synthesis and the gene expression of LOX5 and LOX12 in colonic biopsy samples from healthy individuals (HC) or IBS-D patients. To evaluate the role of gut bacteria in regulating RvD1 synthesis, we colonized germ-free mice with different strains of bacteria, fecal microbiota from HC individuals or IBS-D patients. To evaluate the role of tuft cells in RvD1 synthesis, we examined the effect of fecal supernatant of IBS-D or HC subjects on human colonoids as well as colonoids from mice in which Chat-cre recombinase vector was used to knock-in diphtheria toxin sensitive receptor (DTRf/f) or knock-out the expression of Tlr4f/f or MyD88f/f. ResultsWe report that colonic biopsy samples from IBS-D patients generated significantly lower level of RvD1 and LOX5 mRNA. The conventionalization of germ-free mice with microbiota from IBS-D patients or gram-negative bacteria inhibited RvD1 biosynthesis and caused visceral hypersensitivity and mucosal inflammation. Colonic organoid studies demonstrate that Lps downregulated Lox5 mRNA expression and synthesis of RvD1 via Tlr4-MyD88 receptor signaling pathway in colonic tuft cells. ConclusionsOur findings indicate that RvD1 is generated in colonic tuft cells to regulate gut sensitivity to mechanical stimulation. Colonic commensal bacterial composition regulates the synthesis of RvD1 in colonic mucosa which is reduced in IBS-D patients. This appears to be mediated by elevated fecal lipopolysaccharide secondary to gram-negative gut dysbiosis.

Whole Body Production of Butyrate, but Not of Acetate or Propionate, Is Reduced in Adults With Prediabetes

ObjectivesAccording to the CDC, 38% of the adult US population have prediabetes. Previous studies reported a reduced abundance of butyrate producing bacteria in the colon of participants with prediabetes, potentially contributing to the progression to Type 2 Diabetes. We now studied whether the whole body production of short-chain fatty acids (SCFA: acetate, propionate, butyrate) are altered in middle aged/older adults with prediabetes. MethodsWe measured SCFA kinetics in 12 prediabetic (fasting glucose: 5.7–6.5 mM) and 25 healthy (fasting glucose < 5.7 mM) subjects, 40 years or older. In the fasted state, a pulse containing acetate[13C2], propionate[1-13C] and butyrate[1-13C] was administered intravenously while blood was sampled 4 times over a 30 min period. We measured tracer enrichments in plasma by GC-MS, whole body SCFA production from the area under the curve (AUC) and statistics by ANCOVA corrected for age, sex, and lean body mass as covariates with significance set at P< 0.05 and results expressed as means [95% CI]. ResultsThe prediabetic subjects had a lower butyrate WBP (362 [270, 454] vs. 534 [403, 665] μmol/h, P = 0.021) while acetate WBP (18996 [15270, 23631] vs. 17431 [13478, 22544] μmol/h, P = 0.6049) and propionate WBP (1250 [1041, 1459] vs. 1322 [1053, 1590] μmol/h, P = 0.6624) were comparable. Plasma SCFA concentrations did not differ between the groups (all P >0.05). ConclusionsThe reduced whole body production of butyrate observed in the prediabetic middle aged/older adults is probably related to the altered colonic bacterial composition. More research is required whether specific nutritional modulation of the colonic bacterial composition (e.g. fiber supplementation) is able to restore the butyrate WBP and can improve glucose control in adults with prediabetes. Funding SourcesNone

Differential Effects of Early-Life and Postweaning Galacto-oligosaccharide Intervention on Colonic Bacterial Composition and Function in Weaning Piglets.

Recently, we proved that the early-life galacto-oligosaccharides (GOS) intervention could improve the colonic function by altering the bacterial composition in suckling piglets. However, whether the early-life GOS (ELG) intervention could have a long influence on the colonic microbiota and whether the combined ELG and postweaning GOS (PWG) intervention would have an interacting effect on maintaining colonic health in weaning piglets remain to be explored. In this study, we illustrated the differential effects of the ELG and PWG interventions on colonic microbiota and colonic function of weaning piglets. Our results showed that the ELG and PWG interventions decreased the frequency of diarrhea in weaning piglets while the PWG intervention increased colonic indexes. After 16S rRNA gene MiSeq sequencing of the gut bacteria belonging to different colonic niches (mucosa and digesta), the increase in the α-diversity of the colonic mucosal bacteria during PWG intervention was revealed. In addition, we found that both the ELG and PWG interventions enriched the relative abundances of short-chain fatty acid (SCFA) producers in different colonic niches and increased the total SCFA concentration in colonic digesta. These changes selectively modulated the mRNA expression levels of pattern recognition receptors and barrier proteins in the colonic mucosa. Of note, the combined effect of ELG and PWG effectively enhanced colonic SCFA producer enrichment and upregulated the butyrate concentration. Meanwhile, the expression levels of MyD88-NF-κB signaling and the proinflammatory cytokines were markedly reduced under the combined effect of ELG and PWG. IMPORTANCE Reducing the disorders of the gut ecosystem is an effective way to relieve weaning stresses of piglets and minimize economic losses in the modern swine industry. To this end, prebiotics have been often added to their diet during the weaning transition. In the present study, we demonstrated that the ELG and PWG interventions showed different effects on the bacterial composition of different colonic niches and on colonic function in the weaning piglets. Especially under the combined effect of ELG and PWG intervention, the expression levels of MyD88-NF-κB and the proinflammatory cytokines decreased with increasing concentrations of butyrate, which is an important microbial metabolite involved in the colon of weaning piglets. These findings further provided new insights into nutritional interventions that alleviate intestinal ecosystem dysbiosis and gut dysfunction in the piglets during the weaning transition.

Dietary fat quality impacts metabolic impairments of type 2 diabetes risk differently in male and female CD-1® mice.

Metabolic impairments associated with type 2 diabetes, including insulin resistance and loss of glycaemic control, disproportionately impact the elderly. Lifestyle interventions, such as manipulation of dietary fat quality (i.e. fatty acid (FA) composition), have been shown to favourably modulate metabolic health. Yet, whether or not chronic consumption of beneficial FAs can protect against metabolic derangements and disease risk during ageing is not well defined. We sought to evaluate whether long-term dietary supplementation of fish-, dairy- or echium-derived FAs to the average FA profile in a U.S. American diet may offset metabolic impairments in males and females during ageing. One-month-old CD-1® mice were fed isoenergetic, high-fat (40 %) diets with the fat content composed of either 100 % control fat blend (CO) or 70 % CO with 30 % fish oil, dairy fat or echium oil for 13 months. Every 3 months, parameters of glucose homoeostasis were evaluated via glucose and insulin tolerance tests. Glucose tolerance improved in males consuming a diet supplemented with fish oil or echium oil as ageing progressed, but not in females. Yet, females were more metabolically protected than males regardless of age. Additionally, Spearman correlations were performed between indices of glucose homoeostasis and previously reported measurements of diet-derived FA content in tissues and colonic bacterial composition, which also revealed sex-specific associations. This study provides evidence that long-term dietary fat quality influences risk factors of metabolic diseases during ageing in a sex-dependent manner; thus, sex is a critical factor to be considered in future dietary strategies to mitigate type 2 diabetes risk.

Therapeutic potential of an intestinotrophic hormone, glucagon-like peptide 2, for treatment of type 2 short bowel syndrome rats with intestinal bacterial and fungal dysbiosis

BackgroundPrevious studies showed that type 2 short bowel syndrome (SBS) rats were accompanied by severe intestinal bacterial dysbiosis. Limited data are available for intestinal fungal dysbiosis. Moreover, no effective therapeutic drugs are available for these microbiota dysbiosis. The aims of our study were to investigate the therapeutic potential of glucagon-like peptide 2 (GLP-2) for these microbiota dysbiosis in type 2 SBS rats.Methods8-week-old male SD rats which underwent 80% small bowel resection, ileocecum resection, partial colon resection and jejunocolostomy, were treated with saline (SBS group, n = 5) or GLP-2 (GLP2.SBS group, n = 5). The Sham group rats which underwent transection and re-anastomosis were given a saline placebo (Sham group, n = 5). 16S rRNA and ITS sequencing were applied to evaluate the colonic bacterial and fungal composition at 22 days after surgery, respectively.ResultsThe relative abundance of Actinobacteria, Firmicutes and proinflammatory Proteobacteria increased significantly in SBS group rats, while the relative abundance of Bacteroidetes, Verrucomicrobia and Tenericutes decreased remarkably. GLP-2 treatment significantly decreased Proteus and increased Clostridium relative to the saline treated SBS rats. The diversity of intestinal fungi was significantly increased in SBS rats, accompanied with some fungi abnormally increased and some resident fungi (e.g., Penicillium) significantly decreased. GLP-2 treatment significantly decreased Debaryomyces and Meyerozyma, and increased Penicillium. Moreover, GLP-2 partially restored the bacteria-fungi interkingdom interaction network of SBS rats.ConclusionOur study confirms the bacterial and fungal dysbiosis in type 2 SBS rats, and GLP-2 partially ameliorated these microbiota dysbiosis.

Retraction Note: Deficiency in intestinal epithelial Reg4 ameliorates intestinal inflammation and alters the colonic bacterial composition

This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1038/s41385-020-00367-2.

Undernutrition shifted colonic fermentation and digest-associated bacterial communities in pregnant ewes.

The objective of this study was to evaluate the effect of undernutrition on colonic microbiota and fermentation in pregnant ewes. Sixteen ewes bearing multiple fetuses for 115days in the control (CON) and severe feed restriction (SFR) groups were fed 100% and 30% level of ad libitum feed intake, respectively. After 15-day treatment, all ewes were sacrificed to collect colonic digesta samples to extract DNA for 16S rRNA sequencing and to detect fermentation parameters. Our data showed that SFR increased (P < 0.05) the levels of colonic propionate, isobutyrate, butyrate, isovalerate, and valerate, and slightly decreased (P < 0.1) colonic pH. The mole proportions of isobutyrate, butyrate, and isovalerate were increased (P < 0.05) upon SFR while that of acetate was decreased (P < 0.05). Hematoxylin-eosin staining sections exhibited the disorderly, irregular, and loose arrangement and part sloughing of colonic epithelial cells. Furthermore, SFR decreased (P < 0.05) the diversity of colonic microbiota and changed the microbial communities. At the genus level, SFR increased (P < 0.05) the abundance of unclassified Peptococcaceae and decreased (P < 0.05) the abundances of Ruminococcus, unclassified Ruminococcaceae, and unclassified VadinBB60. Additionally, the abundances of Ruminococcus and unclassified Ruminococcaceae were positively correlated (P < 0.05) with the acetate proportion while the abundance of unclassified Peptococcaceae was negatively correlated (P < 0.05) with the percentages of isobutyrate, butyrate, and isovalerate. In summary, SFR diminished the diversity of bacteria, affected the composition of bacterial communities, and finally changed the colonic fermentation pattern and epithelial histomorphology in pregnant ewes. KEY POINTS: • Undernutrition changed colonic bacterial diversity and composition in pregnant ewes. • Microbial alteration affected colonic fermentation pattern and parameters. • Alteration of colonic microbiota and fermentation damaged epithelium histomorphology. Graphical abstract.

Colonic bacterial composition is sex-specific in aged CD-1 mice fed diets varying in fat quality.

Evidence suggests that sex influences the effect of diet on the gut bacterial composition, yet, no studies have been performed assessing dietary fatty acid composition (i.e., fat quality) in this context. This study examined the effect of dietary fat quality on colonic bacterial composition in an aged, genetically-diverse mouse population. CD-1 mice were fed isoenergetic diets consisting of (1) control fat (CO; “Western-style” fat blend), (2) CO supplemented with 30% fish oil, (3) CO supplemented with 30% dairy fat, or (4) CO supplemented with 30% echium oil. Fecal samples were collected at mid-life and aged (reproductively senescent) time points. Overall, the abundance of Bacteroidetes was greater in mice fed echium oil compared to mice fed the control fat. Examination of colonic bacterial relative abundance also revealed sex differences, with 73 bacterial taxa being differentially expressed in males and females. Notably, results showed a strong interactive effect among the diet, sex, and age of mice which influenced colonic bacterial relative abundance and alpha diversity. In males, supplementation of the diet with dairy fat or echium oil caused the abundance of Bacteroidetes and Bacteroides to change with age. Additionally, supplementation of the diet with fish oil induced sex-dependent changes in the alpha diversity of aged mice compared to mid-life. This work supports that sex is a critical factor in colonic bacterial composition of an aged, genetically-heterogenous population. Moreover, this study establishes that the effectiveness of dietary interventions for health maintenance and disease prevention via direct or indirect manipulation of the gut microbiota is likely dependent on an individual’s sex, age, and genetic background.

Chemotherapy-induced neuroinflammation is associated with disrupted colonic and bacterial homeostasis in female mice

Chemotherapy treatment negatively affects the nervous and immune systems and alters gastrointestinal function and microbial composition. Outside of the cancer field, alterations in commensal bacteria and immune function have been implicated in behavioral deficits; however, the extent to which intestinal changes are related to chemotherapy-associated behavioral comorbidities is not yet known. Thus, this study identified concurrent changes in behavior, central and peripheral immune activation, colon histology, and bacterial community structure in mice treated with paclitaxel chemotherapy. In paclitaxel-treated mice, increased fatigue and decreased cognitive performance occurred in parallel with reduced microglia immunoreactivity, increased circulating chemokine expression (CXCL1), as well as transient increases in pro-inflammatory cytokine/chemokine (Il-1β, Tnfα, Il-6, and Cxcl1) gene expression in the brain. Furthermore, mice treated with paclitaxel had altered colonic bacterial community composition and increased crypt depth. Relative abundances of multiple bacterial taxa were associated with paclitaxel-induced increases in colon mass, spleen mass, and microglia activation. Although microbial community composition was not directly related to available brain or behavioral measures, structural differences in colonic tissue were strongly related to microglia activation in the dentate gyrus and the prefrontal cortex. These data indicate that the chemotherapeutic paclitaxel concurrently affects the gut microbiome, colonic tissue integrity, microglia activation, and fatigue in female mice, thus identifying a novel relationship between colonic tissue integrity and behavioral responses that is not often assessed in studies of the brain-gut-microbiota axis.

RETRACTED ARTICLE:Deficiency in intestinal epithelial Reg4 ameliorates intestinal inflammation and alters the colonic bacterial composition

The regenerating islet-derived family member 4 (Reg4) in the gastrointestinal tract is up-regulated during intestinal inflammation. However, the physiological function of Reg4 in the inflammation is largely unknown. In the current study, the functional roles and involved mechanisms of intestinal epithelial Reg4 in intestinal inflammation were studied in healthy and inflamed states using human intestinal specimens, an intestinal conditional Reg4 knockout mouse (Reg4ΔIEC) model and dextran sulfate sodium (DSS)-induced colitis model. We showed that the elevated serum Reg4 in pediatric intestinal failure (IF) patients were positively correlated with the serum concentrations of proinflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). In inflamed intestine of IF patients, the crypt base Reg4 protein was increased and highly expressed towards the luminal face. The Reg4 was indicated as a novel target of activating transcription factor 2 (ATF2) that enhanced Reg4 expression during the intestinal inflammation. In vivo, the DSS-induced colitis was significantly ameliorated in Reg4ΔIEC mice. Reg4ΔIEC mice altered the colonic bacterial composition and reduced the bacteria adhere to the colonic epithelium. In vitro, Reg4 was showed to promote the growth of colonic organoids, and that this occurs through a mechanism involving activation of signal transducer and activator of transcription 3 (STAT3). In conclusion, our findings demonstrated intestinal-epithelial Reg4 deficiency protects against experimental colitis and mucosal injury via a mechanism involving alteration of bacterial homeostasis and STAT3 activation.

Association of Colonic Bacterial Composition with Host Physiology is Dependent on Dietary Fat Quality and Sex in Aging CD‐1 Mice

Colonic bacterial composition is critical in the development of metabolic diseases, yet, the significance of specific bacterial taxa in disease risk, pathogenesis, and prevention is not well defined. While it is known that diet, sex, age, and genetic makeup of the host can influence colonic bacterial composition, how these factors interact with the bacteria to affect host physiology is poorly understood. Our study utilized the genetically heterogeneous CD‐1 mouse stock to determine the effect of long‐term dietary fat quality (i.e., fatty acid composition) and sex on colonic bacterial composition (relative abundance and diversity) during aging. For 13 months, starting at the age of four weeks, male and female mice were fed one of four isoenergetic (40% total energy) diets: i) Control, U.S. fat blend (CO; representing the dietary fat quality of the average U.S. American); ii) CO fat blend displaced with 30% fish oil (FO); iii) CO fat blend displaced with 30% dairy (butter) fat (BO); and iv) CO fat blend displaced with 30% echium oil (EO). Feed intake and body weight were measured weekly and monthly, respectively. Glucose and insulin tolerance tests (GTT and ITT, respectively) were performed every three months to assess glucose homeostasis and insulin resistance. Individual fecal samples were collected via metabolic cages at 10.5 months of age (i.e., mid‐life in life course) and 13.5 months of age (i.e., aged period in life course; post‐reproductive senescence). Multivariate Spearman correlations were used to determine associations between colonic bacterial composition and glucose homeostasis and insulin resistance. At mid‐life, relative abundance of Alistipes was positively correlated with weight gain in FO‐fed (r = 0.83; P &lt; 0.05) and BO‐fed (r = 0.76; P &lt; 0.05) mice, whereas the relative abundance of Parabacteroides was positively correlated with weight gain in EO‐fed mice (r = 0.68; P &lt; 0.05). In aged mice, the abundance of Allobaculum and Anaerostipes was associated with improved glucose tolerance in BO‐fed mice, as determined by a reduction in GTT area under the curve (AUC; r = −0.65 and r = −0.58, respectively; P &lt; 0.05). In addition, alpha diversity (Chao1) was associated with improved glucose tolerance (via GTT AUC) in aged EO‐fed mice (r = −0.74; P &lt; 0.05). In females, a negative correlation was found between the relative abundance of Roseburia and Barnesiella and fasting plasma glucose at mid‐life (r = −0.51; P &lt; 0.05) and aged (r = −0.58; P &lt; 0.01) life stages, respectively, indicating that these bacterial taxa may contribute positively to glucose homeostasis. Yet, only in aged males, the abundance of Lactobacillus was correlated with improved fasting plasma glucose (r = −0.65; P &lt; 0.01). Our study suggests that dietary fat quality and sex modulate the association of specific colonic bacterial taxa and metabolic risk factors in CD‐1 mice, and that the effects of certain colonic bacteria on host physiology may change with age of an individual.Support or Funding InformationArmin Grams Memorial Research Award, UVM Robert Larner, M.D. College of Medicine; USDA‐NIFA Hatch Fund (accession number: 1006628).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.

Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.

Changes of Colonic Bacterial Composition in Parkinson's Disease and Other Neurodegenerative Diseases.

In recent years evidence has emerged that neurodegenerative diseases (NDs) are strongly associated with the microbiome composition in the gut. Parkinson’s disease (PD) is the most intensively studied neurodegenerative disease in this context. In this review, we performed a systematic evaluation of the published literature comparing changes in colonic microbiome in PD to the ones observed in other NDs including Alzheimer’s disease (AD), multiple system atrophy (MSA), multiple sclerosis (MS), neuromyelitis optica (NMO) and amyotrophic lateral sclerosis (ALS). To enhance the comparability of different studies, only human case-control studies were included. Several studies showed an increase of Lactobacillus, Bifidobacterium, Verrucomicrobiaceae and Akkermansia in PD. A decrease of Faecalibacterium spp., Coprococcus spp., Blautia spp., Prevotella spp. and Prevotellaceae was observed in PD. On a low taxonomic resolution, like the phylum level, the changes are not disease-specific and are inconsistent. However, on a higher taxonomic resolution like genus or species level, a minor overlap was observed between PD and MSA, both alpha synucleinopathies. We show that standardization of sample collection and analysis is necessary for ensuring the reproducibility and comparability of data. We also provide evidence that assessing the microbiota composition at high taxonomic resolution reveals changes in relative abundance that may be specific to or characteristic of one disease or disease group, and might evolve discriminative power. The interactions between bacterial species and strains and the co-abundances must be investigated before assumptions about the effects of specific bacteria on the host can be made with certainty.

Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs

BackgroundPregnancy is associated with important changes in gut microbiota composition. Dietary factors may affect the diversity, composition, and metabolic activity of the intestinal microbiota. Among amino acids, proline is known to play important roles in protein metabolism and structure, cell differentiation, conceptus growth and development, and gut microbiota re-equilibration in case of dysbiosis.ResultsDietary supplementation with 1% proline decreased (P < 0.05) the amounts of Klebsiella pneumoniae, Peptostreptococcus productus, Pseudomonas, and Veillonella spp. in distal colonic contents than that in the control group. The colonic contents of Butyrivibrio fibrisolvens, Bifidobacterium sp., Clostridium coccoides, Clostridium coccoides-Eubacterium rectale, Clostridium leptum subgroup, Escherichia coli, Faecalibacterium prausnitzii, Fusobacterium prausnitzii, and Prevotella increased (P < 0.05) on d 70 of pregnancy as compared with those on d 45 of pregnancy. The colonic concentrations of acetate, total straight-chain fatty acid, and total short-chain fatty acids (SCFA) in the proline-supplemented group were lower (P < 0.05), and butyrate level (P = 0.06) decreased as compared with the control group. Almost all of the SCFA displayed higher (P < 0.05) concentrations in proximal colonic contents on d 70 of pregnancy than those on d 45 of pregnancy. The concentrations of 1,7-heptyl diamine (P = 0.09) and phenylethylamine (P < 0.05) in proximal colonic contents were higher, while those of spermidine (P = 0.05) and total bioamine (P = 0.06) tended to be lower in the proline-supplemented group than those in the control group. The concentrations of spermidine, spermine, and total bioamine in colonic contents were higher (P < 0.05) on d 70 of pregnancy than those measured on d 45 of pregnancy. In contrast, the concentration of phenylethylamine was lower (P < 0.05) on d 70 than on d 45 of pregnancy.ConclusionThese findings indicate that L-proline supplementation modifies both the colonic microbiota composition and the luminal concentrations of several bacterial metabolites. Furthermore, our data show that both the microbiota composition and the concentrations of bacterial metabolites are evolving in the course of pregnancy. These results are discussed in terms of possible implication in terms of luminal environment and consequences for gut physiology and health.