Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine

Characterization of the Effects of a Novel Probiotic on Salmonella Colonization of a Piglet-Derived Intestinal Microbiota Using Improved Bioreactor

The carriage of Salmonella in pigs is a major concern for the agri-food industry and for global healthcare systems. Humans could develop salmonellosis when consuming contaminated pig products. On the other hand, some Salmonella serotypes could cause disease in swine, leading to economic losses on farms. The purpose of the present study was to characterize the anti-Salmonella activity of a novel Bacillus-based probiotic using a bioreactor containing a piglet-derived intestinal microbiota. Two methods of probiotic administration were tested: a single daily and a continuous dose. Salmonella enumeration was performed using selective agar at T24h, T48h, T72h, T96h and T120h. The DNA was extracted from bioreactor samples to perform microbiome profiling by targeted 16S rRNA gene sequencing on Illumina Miseq. The quantification of short-chain fatty acids (SCFAs) was also assessed at T120h. The probiotic decreased Salmonella counts at T96 for the daily dose and at T120 for the continuous one. Both probiotic doses affected the alpha and beta diversity of the piglet-derived microbiota (p < 0.05). A decrease in acetate concentration and an increase in propionate proportion were observed in the continuous condition. In conclusion, the tested Bacillus-based product showed a potential to modulate microbiota and reduce Salmonella colonization in a piglet-derived intestinal microbiota and could therefore be used in vivo.

Microencapsulated Limosilactobacillus reuteri Encoding Lactoferricin-Lactoferrampin Targeted Intestine against Salmonella typhimurium Infection

Salmonella enterica serovar Typhimurium (S. typhimurium) is an important foodborne pathogen that infects both humans and animals and develops acute gastroenteritis. As porcine intestines are relatively similar to the human ones due to their relatively similar sizes and structural similarity, S. typhimurium causes analogous symptoms in both. Novel strategies for controlling S. typhimurium infection are also desired, such as mucosal-targeted delivery of probiotics and antimicrobial peptides. The bovine lactoferricin-lactoferrampin-encoding Limosilactobacillus reuteri (LR-LFCA) strain improves intestinal barrier function by strengthening the intestinal barrier. Weaned piglets were selected for oral administration of microencapsulated LR-LFCA (microcapsules entrap LR-LFCA into gastro-resistant polymers) and then infected with S. typhimurium for 3 days. We found that orally administering microencapsulated LR-LFCA to weaned piglets attenuated S. typhimurium-induced production of inflammatory factors in the intestinal mucosa by inhibiting the nuclear factor-kappa B (NF-κB) and P38 mitogen-activated protein kinases (MAPK) signaling pathway. Moreover, microencapsulated LR-LFCA administration significantly suppressed the oxidative stress that may correlate with gut microbiota (reduced Salmonella population and increased α-diversity and Lactobacillus abundance) and intestinal function (membrane transport and metabolism). Our work demonstrated that microencapsulated LR-LFCA effectively targeted intestine delivery of Lactobacillus and antimicrobial peptides and modulated gut microbiota and mucosal immunity. This study reveals a novel targeting mucosal strategy against S. typhimurium infection.

Transcriptome and proteome profile of jejunum in chickens challenged with Salmonella Typhimurium revealed the effects of dietary bilberry anthocyanin on immune function

Introduction

The present study investigated the effects of bilberry anthocyanin (BA) on immune function when alleviating Salmonella Typhimurium (S. Typhimurium) infection in chickens.

Methods

A total of 180 newly hatched yellow-feathered male chicks were assigned to three groups (CON, SI, and SI + BA). Birds in CON and SI were fed a basal diet, and those in SI + BA were supplemented with 100 mg/kg BA for 18 days. Birds in SI and SI + BA received 0.5 ml suspension of S. Typhimurium (2 × 109 CFU/ml) by oral gavage at 14 and 16 days of age, and those in CON received equal volumes of sterile PBS.

Results

At day 18, (1) dietary BA alleviated weight loss of chickens caused by S. Typhimurium infection (P < 0.01). (2) Supplementation with BA reduced the relative weight of the bursa of Fabricius (P < 0.01) and jejunal villus height (P < 0.05) and increased the number of goblet cells (P < 0.01) and the expression of MUC2 (P < 0.05) in jejunal mucosa, compared with birds in SI. (3) Supplementation with BA decreased (P < 0.05) the concentration of immunoglobulins and cytokines in plasma (IgA, IL-1β, IL-8, and IFN-β) and jejunal mucosa (IgG, IgM, sIgA, IL-1β, IL-6, IL-8, TNF-α, IFN-β, and IFN-γ) of S. Typhimurium-infected chickens. (4) BA regulated a variety of biological processes, especially the defense response to bacteria and humoral immune response, and suppressed cytokine-cytokine receptor interaction and intestinal immune network for IgA production pathways by downregulating 6 immune-related proteins.

Conclusion

In summary, the impaired growth performance and disruption of jejunal morphology caused by S. Typhimurium were alleviated by dietary BA by affecting the expression of immune-related genes and proteins, and signaling pathways are related to immune response associated with immune cytokine receptors and production in jejunum.

Commensal Bacteria Impact on Intestinal Toll-like Receptor Signaling in Salmonella-Challenged Gnotobiotic Piglets

Gnotobiotic (GN) animals with simple and defined microbiota can help to elucidate host-pathogen interferences. Hysterectomy-derived germ-free (GF) minipigs were associated at 4 and 24 h post-hysterectomy with porcine commensal mucinolytic Bifidobacterium boum RP36 (RP36) strain or non-mucinolytic strain RP37 (RP37) or at 4 h post-hysterectomy with Lactobacillus amylovorus (LA). One-week-old GN minipigs were infected with Salmonella Typhimurium LT2 strain (LT2). We monitored histological changes in the ileum, mRNA expression of Toll-like receptors (TLRs) 2, 4, and 9 and their related molecules lipopolysaccharide-binding protein (LBP), coreceptors MD-2 and CD14, adaptor proteins MyD88 and TRIF, and receptor for advanced glycation end products (RAGE) in the ileum and colon. LT2 significantly induced expression of TLR2, TLR4, MyD88, LBP, MD-2, and CD14 in the ileum and TLR4, MyD88, TRIF, LBP, and CD14 in the colon. The LT2 infection also significantly increased plasmatic levels of inflammatory markers interleukin (IL)-6 and IL-12/23p40. The previous colonization with RP37 alleviated damage of the ileum caused by the Salmonella infection, and RP37 and LA downregulated plasmatic levels of IL-6. A defined oligo-microbiota composed of bacterial species with selected properties should probably be more effective in downregulating inflammatory response than single bacteria.

Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs

Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S. Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson's and Shannon's indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.

Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota

The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. 1) and finishing (Exp. 2) pigs. In Exp. 1 (40 day supplementation), forty-five crossbred weaned pigs were randomly assigned to the 0% (Control), 5%, or 10% IS groups (15 replicates/experimental diet). In Exp. 2 (60 day supplementation), eighteen finishing pigs from Exp. 1 were fed the control diet for 8 weeks before being re-assigned to their original experimental groups and fed with the 0% (Control), 5%, or 10% IS diets (six replicates/experimental diet). Performance parameters were recorded. Ileal and caecal digesta and mucosa were collected at the end of each experiment for microbiota analysis using 16S rRNA gene sequencing (five pigs/experimental diet for Exp. 1 and six pigs/experimental diet for Exp. 2). No significant effects on pig growth parameters were observed in both experiments. In Exp. 1, 5% IS supplementation increased the relative abundance of the Prevotellaceae family, Coprococcus genus, and Alloprevotella rava (OTU_48) and reduced the relative abundance of Lactobacillus genus in the caecum compared to the control and/or 10% IS diets (p < 0.05). In Exp. 2, 5% IS supplementation led to compositionally more diverse and different ileal and caecal microbiota compared to the control group (p < 0.05; p = 0.066 for β-diversity in ileum). Supplementation with the 5% IS increased the relative abundance of Clostridium celatum/disporicum/saudiense (OTU_3) in the ileum and caecum and Bifidobacterium pseudolongum (OTU_17) in the caecum and reduced the relative abundance of Streptococcus gallolyticus/alactolyticus (OTU_2) in the caecum compared to the control diet (p < 0.05). Similar effects on C. celatum/disporicum/saudiense and S. gallolyticus/alactolyticus were observed with the 10% IS diet in the caecum (p < 0.05). IS has the potential to beneficially alter the composition of the gastrointestinal microbiota in pigs.

Raw potato starch diet supplement in weaned pigs could reduce Salmonella Typhimurium infection by altering microbiome composition and improving immune status

Backgorund

Salmonella enterica serovar Typhimurium (ST) is one of the causative agents of gastroenteritis in pigs. Pigs fed a diet supplemented with raw potato starch (RPS) have improved gut health by the alteration of the microbiota composition and production of short-chain fatty acids (SCFAs). This study aimed to evaluate the effects of RPS supplementation in reducing infection severity and fecal shedding in ST-infected pigs.

Methods

The weaned experimental pigs were divided into two groups: CON (n = 6) fed a corn/soybean-based diet and TRT (n = 6) supplemented with 5% RPS. After 21 d, the pigs were inoculated with ST, and their body weight, clinical signs, and fecal shedding of ST were monitored for 14 d. At 14 d post-inoculation (dpi), the jejunum, cecum, ileum, and colon tissues were collected from euthanized pigs, and histopathological lesions and cytokine gene expression were compared. Additionally, blood samples at 2 dpi were analyzed for gene ontology enrichment. Moreover, the gutmicrobiome was analyzed using 16S rRNA metagenomic sequencing, and the SCFA concentration was measured using gas chromatography.

Results

The average daily weight gain was significantly higher in TRT than in CON during the ST infection period; however, histopathological lesion scores were significantly lower in TRT than in CON. The relative abundance of nine genera of butyrate- and acetate-producing bacteria significantly increased in TRT compared with that of only two acetate-producing bacteria in CON. Among the genes involved in the immune response, IL-18 expression level was significantly lower in the jejunum and colon in TRT than in CON. Furthermore, Reg3γ expression was significantly different in the cecum and colon of both groups.

Conclusion

The diet supplemented with RPS in weaned pigs could result in predominance of butyrate- and acetate-producing bacteria, reducing the severity of ST infection by improving the immune status.

Weaning stress and intestinal health of piglets: A review

Weaning is considered to be one of the most critical periods in pig production, which is related to the economic benefits of pig farms. However, in actual production, many piglets are often subjected to weaning stress due to the sudden separation from the sow, the changes in diet and living environment, and other social challenges. Weaning stress often causes changes in the morphology and function of the small intestine of piglets, disrupts digestion and absorption capacity, destroys intestinal barrier function, and ultimately leads to reduced feed intake, increased diarrhea rate, and growth retardation. Therefore, correctly understanding the effects of weaning stress on intestinal health have important guiding significance for nutritional regulation of intestinal injury caused by weaning stress. In this review, we mainly reviewed the effects of weaning stress on the intestinal health of piglets, from the aspects of intestinal development, and intestinal barrier function, thereby providing a theoretical basis for nutritional strategies to alleviate weaning stress in mammals in future studies.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

Streptococcus gallolyticus and Bacterial Endocarditis in Swine, United States, 2015-2020

To evaluate trends in bacterial causes of valvular endocarditis in swine, we retrospectively analyzed 321 cases diagnosed at Iowa State University Veterinary Diagnostic Laboratory (Ames, IA, USA) during May 2015--April 2020. Streptococcus gallolyticus was the causative agent for 7.59% of cases. This emerging infection in swine could aid study of endocarditis in humans.

A Predictive Model Based on the Gut Microbiota Improves the Diagnostic Effect in Patients With Cholangiocarcinoma

Cholangiocarcinoma (CCA) is a malignant hepatic tumor with a poor prognosis, which needs early diagnosis urgently. The gut microbiota has been shown to play a crucial role in the progression of liver cancer. Here, we explored a gut microbiota model covering genera Burkholderia-Caballeronia-Paraburkholderia, Faecalibacterium, and Ruminococcus_1 (B-F-R) for CCA early diagnosis. A case-control study was conducted to enroll 53 CCA patients, 47 cholelithiasis patients, and 40 healthy controls. The feces samples and clinical information of participants were collected in the same period. The gut microbiota and its diversity of individuals were accessed with 16S rDNA sequencing, and the gut microbiota profile was evaluated according to microbiota diversity. Finally, four enriched genera in the CCA group (genera Bacteroides, Muribaculaceae_unclassified, Muribaculum, and Alistipes) and eight enriched genera in the cholelithiasis group (genera Bifidobacterium, Streptococcus, Agathobacter, Ruminococcus_gnavus_group, Faecalibacterium, Subdoligranulum, Collinsella, Escherichia-Shigella) constitute an overall different microbial community composition (P = 0.001). The B-F-R genera model with better diagnostic value than carbohydrate antigen 19-9 (CA19-9) was identified by random forest and Statistical Analysis of Metagenomic Profiles (STAMP) to distinguish CCA patients from healthy controls [area under the curve (AUC) = 0.973, 95% CI = 0.932–1.0]. Moreover, the correlative analysis found that genera Burkholderia-Caballeronia-Paraburkholderia were positively correlated with body mass index (BMI). The significantly different microbiomes between cholelithiasis and CCA were found via principal coordinates analysis (PCoA) and linear discriminant analysis effect size (LEfSe), and Venn diagram and LEfSe were utilized to identify four genera by comparing microbial compositions among patients with malignant obstructive jaundice (MOJ-Y) or not (MOJ-N). In brief, our findings suggest that gut microbiota vary from benign and malignant hepatobiliary diseases to healthy people and provide evidence supporting gut microbiota to be a non-invasive biomarker for the early diagnosis of CCA.

Local and Systemic T Cell Immunity in Fighting Pig Viral and Bacterial Infections

T cells are an essential component of the adaptive immune system. Over the last 15 years, a constantly growing toolbox with which to study T cell biology in pigs has allowed detailed investigations on these cells in various viral and bacterial infections. This review provides an overview on porcine CD4, CD8, and γδ T cells and the current knowledge on the differentiation of these cells following antigen encounter. Where available, the responses of these cells to viral infections like porcine reproductive and respiratory syndrome virus, classical swine fever virus, swine influenza A virus, and African swine fever virus are outlined. In addition, knowledge on the porcine T cell response to bacterial infections like Actinobacillus pleuropneumoniae and Salmonella Typhimurium is reviewed. For CD4 T cells, the response to the outlined infections is reflected toward the Th1/Th2/Th17/Tfh/Treg paradigm for functional differentiation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The comparative pathology of enterocolitis caused by Clostridium perfringens type C, Clostridioides difficile, Paeniclostridium sordellii, Salmonella enterica subspecies enterica serovar Typhimurium, and nonsteroidal anti-inflammatory drugs in horses

To determine if there were significant differences produced by 5 of the most prevalent causes of equine enterocolitis, we studied retrospectively the gross and microscopic pathology of 90 cases of enterocolitis submitted to the San Bernardino laboratory of the California Animal Health and Food Safety Laboratory. Included were cases caused by Clostridium perfringens type C (CP; n = 20), Clostridioides difficile (CD; n = 20), Paeniclostridium sordellii (PS; n = 15), Salmonella enterica subspecies enterica serovar Typhimurium (ST; n = 20), and NSAID intoxication (NS; n = 15). Grossly, necrotizing hemorrhagic typhlocolitis was seen most frequently in cases of CD, ST, and NS disease. Cases of CP and PS had enteritis or colitis in similar percentages. Congestion, hemorrhage, and pleocellular inflammatory infiltrates followed by mucosal and submucosal necrosis were the main lesions found in horses with enteritis or colitis produced by any of the etiologic agents investigated. Severe lesions were more frequent in cases of CD and CP than in cases associated with any of the other 3 etiologies. Pseudomembranes were observed with similar prevalence in the small intestine and colon affected by all agents studied. Thrombosis of the lamina propria and/or submucosa was observed in ~50% of the cases of enteritis and colitis by all etiologies, except for PS, in which the majority of the cases had thrombosis. Gross and microscopic lesions of enterocolitis were not sufficiently specific for any of these etiologic agents to enable these enteritides to be distinguished by gross and/or histologic examination.

Protective Effects of Cinnamaldehyde on the Inflammatory Response, Oxidative Stress, and Apoptosis in Liver of Salmonella typhimurium-Challenged Mice

Salmonella typhimurium infection is associated with gastrointestinal disorder and cellular injury in the liver of both humans and animals. Cinnamaldehyde, the main component of essential oil from cinnamon, has been reported to have anti-inflammatory, anti-oxidative, and anti-apoptotic effects. However, it remains unknown whether cinnamaldehyde can alleviate Salmonella typhimurium infection-induced liver injury in mice. In the present study, we found that cinnamaldehyde attenuated Salmonella typhimurium-induced body weight loss, the increase of organ (liver and spleen) indexes, hepatocyte apoptosis, and the mortality rate in mice. Further study showed that cinnamaldehyde significantly alleviated Salmonella typhimurium-induced liver injury as shown by activities of alanine transaminase, aspartate transaminase, and myeloperoxidase, as well as malondialdehyde. The increased mRNA level of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α, and IFN-γ) and chemokines (CCL2 and CCL3) induced by Salmonella typhimurium were significantly abolished by cinnamaldehyde supplementation. These alterations were associated with a regulatory effect of cinnamaldehyde on TLR2, TLR4, and MyD88. 16S rDNA sequence analysis showed that Salmonella typhimurium infection led to upregulation of the abundances of genera Akkermansia, Bacteroides, Alistipes, Muribaculum, and Prevotellaceae UCG-001, and downregulation of the abundances of genera Lactobacillus, Enterorhabdus, and Eggerthellaceae (unclassified). These alterations were reversed by cinnamaldehyde supplementation. In conclusion, cinnamaldehyde attenuated the inflammatory response, oxidative stress, and apoptosis in the liver of Salmonella typhimurium-infected mice. Supplementation of cinnamaldehyde might be a preventive strategy to alleviate liver injury caused by Salmonella typhimurium infection in humans and animals.

Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine

The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals.IMPORTANCE This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.