Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon

Isolation of mucosa-associated microbiota dysbiosis in the ascending colon in hepatitis C virus post-sustained virologic response cirrhotic patients

Background

Achieving sustained virologic response (SVR) in patients infected with hepatitis C virus (HCV) reduces all-cause mortality. However, the mechanisms and risk factors for liver fibrosis and portal hypertension post-SVR remain incompletely understood. In the gut-liver axis, mucosa-associated microbiota (MAM) substantially influence immune and metabolic functions, displaying spatial heterogeneity at the anatomical intestinal site. We analyzed MAM composition and function to isolate the locoregional MAM involved in chronic liver disease progression in HCV post-SVR patients.

Methods

We collected MAM samples from three intestinal sites (terminal ileum, ascending colon, and sigmoid colon) via brushing during colonoscopy in 23 HCV post-SVR patients and 25 individuals without liver disease (controls). The 16S rRNA of bacterial DNA in specimens collected with a brush and in feces was sequenced. The molecular expression of intestinal tissues and hepatic tissues were evaluated by quantitative real-time PCR.

Results

In the post-SVR group, the microbial β-diversity of MAM, especially in the ascending colon, differed from the control group and was associated with liver fibrosis progression. In PICRUSt analysis, MAM in the ascending colon in the liver cirrhosis (LC) group showed compromised functions associated with the intestinal barrier and bile acid production, and FGF19 expression was markedly decreased in the terminal ileum biopsy tissue in the LC group. At the genus level, six short-chain fatty acid (SCFA)-producing bacterial genera, Blautia, Alistipes, Roseburia, Agathobaculum, Dorea, and Pseudoflavonifractor were reduced in the ascending colon of post-SVR LC patients.

Conclusion

In patients of HCV post-SVR, we identified the association between the degree of liver fibrosis and dysbiosis of mucosa-associated SCFA-producing bacterial genera that may be related to intestinal barrier and bile acid production in the ascending colon.

Host-pathogen interactions from a metabolic perspective: methods of investigation

Metabolism shapes immune homeostasis in health and disease. This review presents the range of methods that are currently available to investigate the dialog between metabolism and immunity at the systemic, tissue and cellular levels, particularly during infection.

Does the microbiome play a role in the pathogenesis of colonic diverticular disease? A systematic review

BACKGROUND AND AIMS

The role of the microbiota in diverticulosis and diverticular disease is underexplored. This systematic review aimed to assess all literature pertaining to the microbiota and metabolome associations in asymptomatic diverticulosis, symptomatic uncomplicated diverticular disease (SUDD), and diverticulitis pathophysiology.

METHODS

Seven databases were searched for relevant studies published up to September 28, 2022. Data were screened in Covidence and extracted to Excel. Critical appraisal was undertaken using the Newcastle Ottawa Scale for case/control studies.

RESULTS

Of the 413 papers screened by title and abstract, 48 full-text papers were reviewed in detail with 12 studies meeting the inclusion criteria. Overall, alpha and beta diversity were unchanged in diverticulosis; however, significant changes in alpha diversity were evident in diverticulitis. A similar Bacteroidetes to Firmicutes ratio compared with controls was reported across studies. The genus-level comparisons showed no relationship with diverticular disease. Butyrate-producing microbial species were decreased in abundance, suggesting a possible contribution to the pathogenesis of diverticular disease. Comamonas species was significantly increased in asymptomatic diverticulosis patients who later developed diverticulitis. Metabolome analysis reported significant differences in diverticulosis and SUDD, with upregulated uracil being the most consistent outcome in both. No significant differences were reported in the mycobiome.

CONCLUSION

Overall, there is no convincing evidence of microbial dysbiosis in colonic diverticula to suggest that the microbiota contributes to the pathogenesis of asymptomatic diverticulosis, SUDD, or diverticular disease. Future research investigating microbiota involvement in colonic diverticula should consider an investigation of mucosa-associated microbial changes within the colonic diverticulum itself.

Atypical behavioral and thermoregulatory circadian rhythms in mice lacking a microbiome

Trillions of microbial oscillators reside throughout the mammalian body, yet their contributions toward fundamental features of host circadian rhythms (CRs) have not been characterized. Here, we demonstrate that the microbiome contributes to host CRs in activity and thermoregulation. Mice devoid of microbes (germ-free, GF) exhibited higher-amplitude CRs in a light-dark cycle and longer circadian periods in constant darkness. Circadian entrainment to food was greater in GF mice, but resetting responses to simulated jet-lag were unaffected. Microbial transplantation with cecal contents of conventionally-raised mice normalized CRs of GF mice, indicating that the concurrent activity of gut microbes modulates host circadian networks. Obesogenic effects of high-fat diet were absent in GF mice, but some circadian-disruptive effects persisted. Transkingdom (host-microbe) interactions affect circadian period and entrainment of CRs in diverse traits, and microbes alter interactions among light- and food-entrainable circadian processes in the face of environmental (light, diet) perturbations.

A pilot study demonstrating the impact of surgical bowel preparation on intestinal microbiota composition following colon and rectal surgery

The intestinal microbiota has been implicated in the pathogenesis of complications following colorectal surgery, yet perioperative changes in gut microbiome composition are poorly understood. The objective of this study was to characterize the perioperative gut microbiome in patients undergoing colonoscopy and colorectal surgery and determine factors influencing its composition. Using Illumina amplicon sequencing coupled with targeted metabolomics, we characterized the fecal microbiota in: (A) patients (n = 15) undergoing colonoscopy who received mechanical bowel preparation, and (B) patients (n = 15) undergoing colorectal surgery who received surgical bowel preparation, composed of mechanical bowel preparation with oral antibiotics, and perioperative intravenous antibiotics. Microbiome composition was characterized before and up to six months following each intervention. Colonoscopy patients had minor shifts in bacterial community composition that recovered to baseline at a mean of 3 (1–13) days. Surgery patients demonstrated substantial shifts in bacterial composition with greater abundances of Enterococcus, Lactobacillus, and Streptococcus. Compositional changes persisted in the early postoperative period with recovery to baseline beginning at a mean of 31 (16–43) days. Our results support surgical bowel preparation as a factor significantly influencing gut microbial composition following colorectal surgery, while mechanical bowel preparation has little impact.

Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine

Gut microbiomics is based on analysis of both live and dead cells in the stool. However, to understand the ecology of gut microbiota and their symbiotic relationships with hosts, spatial distribution of live bacteria must be examined. Here, we analyzed the live composition of luminal microbiota (LM) and mucosa-associated microbiota (MAM) in the ascending and descending colons and the rectums of 10 healthy adults and compared it with the total composition. The abundance of Lachnospiraceae in live LM decreased along the gut length and was significantly lower than that in total LM. Contrastingly, the abundance of Bacteroidaceae and Bifidobacteriaceae in live LM was higher than that in total LM, suggesting differences in death rate during gut migration. Live Enterobacteriaceae levels in MAM were significantly higher in rectum than in the ascending and descending colons and in LM. High-performance liquid chromatographic analysis of luminal bile acids revealed that 7α-dehydroxylation occurred towards the rectum. In live LM where a bile acid-inducible gene could be detected, 7α-dehydroxylation rates were higher than those in the group without the gene. Overall, we showed differences in live bacteria composition among three gut sites and between LM and MAM, highlighting the importance of understanding their spatial distribution.

Simulation of the mucosal environment in the re-construction of the synthetic gut microbial ecosystem

Human gut surface-attached mucosal microbiota plays significant roles in human health and diseases. This study sought to simulate the mucosal environment using mucin-agar gel and synthetic mucosal microbial community in vitro. To select suitable culture media, microbial communities were assembled and cultured in seven different media at 37 °C for 36 h. Among the seven media, Bryant & Burkey (BB) and Gifu Anaerobic Media (GAM) were selected considering their microbial biomass and bacterial composition. The communities were again assembled and cultured in these two media with mucin-agar. The results showed that some bacterial genus such as Bifidobacterium, Collinsella, and Roseburia could efficiently colonize in the solid mucin-agar part while Enterococcus, Clostridium, and Veilonella dominated in the liquid part. Metabolic functional prediction for the microbial community in each medium part showed that the gene expression involved in metabolism and cell motility pathways were distinctively differentiated between the liquid and solid medium part, and the functional potential was highly related to the microbial composition. The current results demonstrate that the simulation of the gut microbial ecosystem in vitro can be beneficial to the mucosal environment mimicking and the study on the mechanistic potential of the human gut microbiota for easy translation of microbiome research to therapies.

Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections

The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.

The longitudinal and cross-sectional heterogeneity of the intestinal microbiota

A central goal of microbiome research is to understand the factors that balance gut-associated microbial communities, thereby creating longitudinal and cross-sectional heterogeneity in their composition and density. Whereas the diet dictates taxa dominance, microbial communities are linked intimately to host physiology through digestive and absorptive functions that generate longitudinal heterogeneity in nutrient availability. Additionally, the host differentially controls the access to electron acceptors along the longitudinal axis of the intestine to drive the development of microbial communities that are dominated by facultatively anaerobic bacteria in the small intestine or obligately anaerobic bacteria in the large intestine. By secreting mucus and antimicrobials, the host further constructs microhabitats that generate cross-sectional heterogeneity in the colonic microbiota composition. Here we will review how understanding the host factors involved in generating longitudinal and cross-sectional microbiota heterogeneity helps define physiological states that are characteristic of or appropriate to a homeostatic microbiome.

Technological tools and strategies for culturing human gut microbiota in engineered in vitro models

The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.

Gastrointestinal biofilms in health and disease

Microorganisms colonize various ecological niches in the human habitat, as they do in nature. Predominant forms of multicellular communities called biofilms colonize human tissue surfaces. The gastrointestinal tract is home to a profusion of microorganisms with intertwined, but not identical, lifestyles: as isolated planktonic cells, as biofilms and in biofilm-dispersed form. It is therefore of major importance in understanding homeostatic and altered host-microorganism interactions to consider not only the planktonic lifestyle, but also biofilms and biofilm-dispersed forms. In this Review, we discuss the natural organization of microorganisms at gastrointestinal surfaces, stratification of microbiota taxonomy, biogeographical localization and trans-kingdom interactions occurring within the biofilm habitat. We also discuss existing models used to study biofilms. We assess the contribution of the host-mucosa biofilm relationship to gut homeostasis and to diseases. In addition, we describe how host factors can shape the organization, structure and composition of mucosal biofilms, and how biofilms themselves are implicated in a variety of homeostatic and pathological processes in the gut. Future studies characterizing biofilm nature, physical properties, composition and intrinsic communication could shed new light on gut physiology and lead to potential novel therapeutic options for gastrointestinal diseases.

Host/microbiota interactions in health and diseases-Time for mucosal microbiology!

During the last 20 years, a new field of research delineating the importance of the microbiota in health and diseases has emerged. Inappropriate host-microbiota interactions have been shown to trigger a wide range of chronic inflammatory diseases, and defining the exact mechanisms behind perturbations of such relationship, as well as ways by which these disturbances can lead to disease states, both remain to be fully elucidated. The mucosa-associated microbiota constitutes a recently studied microbial population closely linked with the promotion of chronic intestinal inflammation and associated disease states. This review will highlight seminal works that have brought into light the importance of the mucosa-associated microbiota in health and diseases, emphasizing the challenges and promises of expending the mucosal microbiology field of research.

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach

Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host–microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.

Experimental models to study intestinal microbes–mucus interactions in health and disease

A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium. The review starts by setting up the biological context underpinning the need for experimental models to study gut bacteria-mucus interactions in the digestive environment. We provide an overview of the structure and function of intestinal mucus and mucins, their interactions with intestinal bacteria (including commensal, probiotics and pathogenic microorganisms) and their role in modulating health and disease states. We then describe the characteristics and potentials of experimental models currently available to study the mechanisms underpinning the interaction of mucus with gut microbes, including in vitro, ex vivo and in vivo models. We then discuss the limitations and challenges facing this field of research.

Microbiota profile in new-onset pediatric Crohn's disease: data from a non-Western population

Background

The role of microbiota in Crohn’s disease (CD) is increasingly recognized. However, most of the reports are from Western populations. Considering the possible variation from other populations, the aim of this study was to describe the microbiota profile in children with CD in Saudi Arabia, a non-Western developing country population.

Results

Significantly more abundant genera in children with CD included Fusobacterium, Peptostreptococcus, Psychrobacter, and Acinetobacter; whereas the most significantly-depleted genera included Roseburia, Clostridium, Ruminococcus, Ruminoclostridium, Intestinibacter, Mitsuokella, Megasphaera, Streptococcus, Lactobacillus, Turicibacter, and Paludibacter. Alpha diversity was significantly reduced in stool (p = 0.03) but not in mucosa (p = 0.31). Beta diversity showed significant difference in community composition between control and CD samples (p = 0.03).

Conclusion

In this developing country, we found a pattern of microbiota in children with CD similar to Western literature, suggesting a role of recent dietary lifestyle changes in this population on microbiota structure.

Microbiota and metabolism: what's new in 2018?

The concept that the gut microbiota plays a broadly important role in health and disease in general, and metabolic health in particular, is now well established. However, many of the underlying mechanisms remain poorly understood while approaches to reliably manipulate the microbiota to promote health have not yet been clearly defined. Nonetheless, progress in these areas is steadily accelerating. Herein, we review select areas of progress that have been made in the last year that should hasten the era in which the microbiota can be therapeutically manipulated to promote metabolic health.

Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts

Laser microdissection is a method that allows for the isolation of homogenous cell populations from their native niches in tissues for downstream molecular assays. This method is widely used for genomic analysis, gene expression profiling and proteomic and metabolite assays in various fields of biology, but it remains an uncommon approach in microbiological research. In spite of the limited number of publications, laser microdissection was shown to be an extremely useful method for studying host-microorganism interactions in animals and plants, investigating bacteria within biofilms, identifying uncultivated bacteria and performing single prokaryotic cell analysis. The current paper describes the methodological aspects of commercially available laser microdissection instruments and representative examples that demonstrate the advantages of this method for resolving a variety of issues in microbiology.

De Novo Synthesis and Functional Analysis of Polyphosphate-Loaded Poly(Ethylene) Glycol Hydrogel Nanoparticles Targeting Pyocyanin and Pyoverdin Production in Pseudomonas aeruginosa as a Model Intestinal Pathogen

The human gastrointestinal tract is the primary site of colonization of multidrug resistant pathogens and the major source of life-threatening complications in critically ill and immunocompromised patients. Eradication measures using antibiotics carry further risk of antibiotic resistance. Furthermore, antibiotic treatment can adversely shift the intestinal microbiome toward domination by resistant pathogens. Therefore, approaches directed to prevent replacement of health promoting microbiota with resistant pathogens should be developed. The use of non-microbicidal drugs to create microenvironmental conditions that suppress virulence of pathogens is an attractive strategy to minimize the negative consequences of intestinal microbiome disruption. We have previously shown that phosphate is depleted in the intestinal tract following surgical injury, that this depletion is a major "cue" that triggers bacterial virulence, and that the maintenance of phosphate abundance prevents virulence expression. However, the use of inorganic phosphate may not be a suitable agent to deliver to the site of the host-pathogen interaction since it is readily adsorbed in small intestine. Here we propose a novel drug delivery approach that exploits the use of nanoparticles that allow for prolonged release of phosphates. We have synthesized phosphate (Pi) and polyphosphate (PPi) crosslinked poly (ethylene) glycol (PEG) hydrogel nanoparticles (NP-Pi and NP-PPi, respectively) that result in sustained delivery of Pi and PPi. NP-PPi demonstrated more prolonged release of PPi as compared to the release of Pi from NP-Pi. In vitro studies indicate that free PPi as well NP-PPi are effective compounds for suppressing pyoverdin and pyocyanin production, two global virulence systems of virulence of P. aeruginosa. These studies suggest that sustained release of polyphosphate from NP-PPi can be exploited as a target for virulence suppression of lethal pathogenic phenotypes in the gastrointestinal tract.

Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota?

Obesity increases the risk of type 2 diabetes, cardiovascular diseases, and certain cancers, which are among the leading causes of death worldwide. Obesity and obesity-related metabolic diseases are characterized by specific alterations in the human gut microbiota. Experimental studies with gut microbiota transplantations in mice and in humans indicate that a specific gut microbiota composition can be the cause and not just the consequence of the obese state and metabolic disease, which suggests a potential for gut microbiota modulation in prevention and treatment of obesity-related metabolic diseases. In addition, dietary intervention studies have suggested that modulation of the gut microbiota can improve metabolic risk markers in humans, but a causal role of the gut microbiota in such studies has not yet been established. Here, we review and discuss the role of the gut microbiota in obesity-related metabolic diseases and the potential of dietary modulation of the gut microbiota in metabolic disease prevention and treatment.

Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality

The human gut microbiome provides us with functional features that we did not have to evolve ourselves and can be viewed as a structured microbial community that operates like a microbial organ within the human host. A minor but important part of this microbiome is the ability to colonise and thrive within the mucous layer that covers the colon epithelium. These mucosal microbes intimately interact with the intestinal tissue and seem to be important modulators of human health. Embedded in the host-secreted mucous matrix, they form a 'mucosal biofilm' with a distinct composition and functionality. In this review, we provide evidence that six specific (micro)environmental factors near the colon mucosa shape and determine mucosal biofilm formation and stability, that is, (1) mucous rigidity, (2) gradients of fluid shear, (3) radial oxygen gradients, (4) secretions of host defense molecules, (5) the presence of a rich but challenging nutrient platform and (6) the presence of niches at the colon epithelial surface. In addition, it appears that microbes actively participate in shaping their mucosal environment. Current insights into the interaction between mucosal microbes and their environment are rather limited, and many questions regarding the contribution of mucosal biofilm functionality and stability to human health remain to be answered. Yet, given the higher potency of mucosal microbes than their luminal counterparts to interact with the host, new insights can accelerate the development of novel disease-preventive or therapeutic strategies.

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

OBJECTIVES

The relevance of spatial composition in the microbial changes associated with UC is unclear. We coupled luminal brush samples, mucosal biopsies and laser capture microdissection with deep sequencing of the gut microbiota to develop an integrated spatial assessment of the microbial community in controls and UC.

DESIGN

A total of 98 samples were sequenced to a mean depth of 31,642 reads from nine individuals, four control volunteers undergoing routine colonoscopy and five patients undergoing surgical colectomy for medically-refractory UC. Samples were retrieved at four colorectal locations, incorporating the luminal microbiota, mucus gel layer and whole mucosal biopsies.

RESULTS

Interpersonal variability accounted for approximately half of the total variance. Surprisingly, within individuals, asymmetric Eigenvector map analysis demonstrated differentiation between the luminal and mucus gel microbiota, in both controls and UC, with no differentiation between colorectal regions. At a taxonomic level, differentiation was evident between both cohorts, as well as between the luminal and mucosal compartments, with a small group of taxa uniquely discriminating the luminal and mucosal microbiota in colitis. There was no correlation between regional inflammation and a breakdown in this spatial differentiation or bacterial diversity.

CONCLUSIONS

Our study demonstrates a conserved spatial structure to the colonic microbiota, differentiating the luminal and mucosal communities, within the context of marked interpersonal variability. While elements of this structure overlap between UC and control volunteers, there are differences between the two groups, both in terms of the overall taxonomic composition and how spatial structure is ascribable to distinct taxa.

Application of Laser Capture Microdissection and 16S rRNA Gene Polymerase Chain Reaction in the Analysis of Bacteria Colonizing the Intestinal Tissue of Neonates With Necrotizing Enterocolitis

BACKGROUND

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in newborns. However, the pathogenesis of NEC remains unclear because most bacterial characterizations of alleged pathogens have been performed via the analysis of human fecal samples and experimental animal studies. The objective is to investigate the microbial composition of NEC using inflamed intestinal tissue surgically removed from neonates diagnosed with NEC (n = 18).

METHODS

We obtained intestinal tissues via a combination of laser capture microdissection and Gram staining, which was used to mark individual bacteria. Tissues with congenital intestinal atresia (n = 7) served as control specimens. An analysis of the 16S rRNA of each sample was performed via polymerase chain reaction-denaturing gradient gel electrophoresis.

RESULTS

Numerous bacteria were observed in the inflamed intestinal wall tissue samples obtained from neonates with NEC following Gram staining and examination under an optical microscope. The total number of types detected by polymerase chain reaction-denaturing gradient gel electrophoresis was 12.17 ± 2.83 per infant with NEC, whereas only 2.57 ± 1.81 types were detected in each infant with congenital intestinal atresia. Proteobacteria had the highest constituent ratio (188 of 285) of all detected clone sequences in the NEC group. Additionally, Pseudomonas sp., Acinetobacter sp., Klebsiella sp., Clostridium sp., Ochrobactrum sp. and Arcobacter sp. were detected only in the NEC group.

CONCLUSIONS

The combination of Gram staining and laser capture microdissection was a reliable method to obtain and prepare tissue samples for processing. NEC was associated with multiple species of bacteria, and microflora within the disease-affected sites may be relatively specific and stable. Proteobacteria demonstrated the highest constituent ratio. Our observations warrant closer examination of the 6 bacterial genera that were only detected in NEC, particularly Clostridium sp., which may be closely correlated with pneumatosis intestinalis.

The effects of variable sample biomass on comparative metagenomics

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys.

Intestinal anastomotic injury alters spatially defined microbiome composition and function

BACKGROUND

When diseased intestine (i.e., from colon cancer, diverticulitis) requires resection, its reconnection (termed anastomosis) can be complicated by non-healing of the newly joined intestine resulting in spillage of intestinal contents into the abdominal cavity (termed anastomotic leakage). While it is suspected that the intestinal microbiota have the capacity to both accelerate and complicate anastomotic healing, the associated genotypes and functions have not been characterized.

RESULTS

Using 16S rRNA amplicon sequencing of samples collected on the day of surgery (postoperative day 0 (POD0)) and the 6th day following surgery (postoperative day 0 (POD6)), we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats. Results indicated that anastomotic injury induced significant changes in the anastomotic tissue-associated microbiota with minimal differences in the luminal microbiota. The most striking difference was a 500-fold and 200-fold increase in the relative abundance of Enterococcus and Escherichia/Shigella, respectively. Functional profiling predicted the predominance of bacterial virulence-associated pathways in post-anastomotic tissues, including production of hemolysin, cytolethal toxins, fimbriae, invasins, cytotoxic necrotizing factors, and coccolysin.

CONCLUSION

Taken together, our results suggest that compositional and functional changes accompany anastomotic tissues and may potentially accelerate or complicate anastomotic healing.

Mina53, a novel molecular marker for the diagnosis and prognosis of gastric adenocarcinoma

Mina53 is a direct novel target protein of Myc. The present study investigated the expression of mina53 and c-myc in gastric carcinoma and the relationship between Mina53 expression and clinicopathological features. The expression levels of mina53 and c-myc mRNA and protein in gastric cancers and the adjacent normal tissues from 12 patients were assessed by laser-capture microdissection (LCM) combined with quantitative polymerase chain reaction (qPCR) and western blotting, respectively. Immunohistochemical analysis was used to evaluate the expression of the Mina53 protein in normal gastric tissues (n=30), chronic atrophic gastritis without intestinal metaplasia (n=44), intestinal metaplasia (n=34), gastric dysplasia (n=36), intestinal-type gastric carcinoma (IGC) (n=30) and diffuse-type gastric carcinoma (DGC) (n=34). The correlation between expression of mina53 and patient survival time was also investigated. The expression levels of mina53 and c-myc mRNA in the gastric carcinomas were found to be higher when compared to these levels in the adjacent normal tissues. In addition, the expression levels of Mina53 and c-Myc protein in gastric carcinomas were higher when compared with levels in the adjacent normal epithelium. mina53 expression was significantly increased during gastric carcinogenesis and was correlated with different clinicopathological factors in IGC and DGC. The prognosis of patients with low expression of Mina53 was more favorable when compared to the prognosis of patients with high expression of Mina53. mina53 expression was gradually elevated during gastric carcinogenesis, and the overexpression of mina53 was correlated with different clinicopathological features between DGC and IGC cases. Furthermore, the prognosis of gastric carcinoma patients was significantly correlated with the expression of Mina53.

Identification of a microscopically selected microorganism in milk samples

Identification of unwanted microbial contaminants microscopically observed in food products is challenging due to their low abundance in a complex matrix, quite often containing other microorganisms. Therefore, a selective identification method was developed using laser capture microdissection in combination with direct-captured cell PCR. This procedure was validated with Geobacillus stearothermophilus and further used to identify microbial contaminants present in some industrial milk samples. The microscopically observed contaminants were identified as mainly Methylobacterium species.

Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota

The unique anatomy and physiology of the intestine in conjunction with its microbial content create the steepest oxygen gradients in the body, which plunge to near anoxia at the luminal midpoint. Far from static, intestinal oxygen gradients ebb and flow with every meal. This in turn governs the redox effectors nitric oxide, hydrogen sulfide, and reactive oxygen species of both host and bacterial origin. This review illustrates how the intestine and microbes utilize oxygen gradients as a backdrop for mechanistically shaping redox relationships and a functional coexistence.

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.

During critical illness the gut does not pass the acid test

The composition and function of intestinal microflora are emerging as integral to both health and disease. During critical illness the normal microbiota are rapidly replaced by pathogenic species as a result of both the physiologic stress itself and the use of antibiotics. In this report, the authors use fecal pH as a surrogate marker to determine the predictive value of the functional output of the intestinal microflora during critical illness. Fecal pH appears to be highly predictive of outcome from critical illness, and may reflect the output of key organic acids such as the short-chain fatty acids, lactic acid, and other important products of the gut microflora.

The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen

Background

Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation.

Methods

Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA) software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene.

Results

B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function “receptor activity”, most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats.

Conclusions

B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to the identification of novel microbial targets for IBD therapies.

A method for metagenomics of Helicobacter pylori from archived formalin-fixed gastric biopsies permitting longitudinal studies of carcinogenic risk

The human microbiota has come into focus in the search for component causes of chronic diseases, such as gastrointestinal cancers. Presumably long induction periods and altered local environments after disease onset call for the development of methods for characterization of microorganisms colonizing the host decades before disease onset. Sequencing of microbial genomes in old formalin-fixed and paraffin-embedded (FFPE) gastrointestinal biopsies provides a means for such studies but is still challenging. Here we report a method based on laser capture micro-dissection and modified Roche 454 high-throughput pyrosequencing to obtain metagenomic profiles of Helicobacter pylori. We applied this method to two 15 year old FFPE biopsies from two patients. Frozen homogenized biopsies from the same gastroscopy sessions were also available for comparison after re-culture of H. pylori. For both patients, H. pylori DNA dissected from FFPE sections had ∼96.4% identity with culture DNA from the same patients, while only ∼92.5% identity with GenBank reference genomes, and with culture DNA from the other patient. About 82% and 60% of the predicted genes in the two genomes were captured by at least a single sequencing read. Along with sequences displaying high similarity to known H. pylori genes, novel and highly variant H. pylori sequences were identified in the FFPE sections by our physical enrichment approach, which would likely not have been detected by a sequence capture approach. The study demonstrates the feasibility of longitudinal metagenomic studies of H. pylori using decade-preserved FFPE biopsies.

Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward

In this commentary, we will review some of the early efforts aimed at understanding the role of the enteric microbiota in the causality of inflammatory bowel diseases. By examining these studies and drawing on our own experiences bridging clinical gastroenterology and microbial ecology as part of the NIH-funded Human Microbiome Project (Turnbaugh et al., 2007), we hope to help define some of the “growing pains” that have hampered these initial efforts. It is our sincere hope that this discussion will help advance future efforts in this area by identifying current challenges and limitations and by suggesting strategies to overcome these obstacles.

Interaction of Salmonella spp. with the Intestinal Microbiota

Salmonella spp. are major cause of human morbidity and mortality worldwide. Upon entry into the human host, Salmonella spp. must overcome the resistance to colonization mediated by the gut microbiota and the innate immune system. They successfully accomplish this by inducing inflammation and mechanisms of innate immune defense. Many models have been developed to study Salmonella spp. interaction with the microbiota that have helped to identify factors necessary to overcome colonization resistance and to mediate disease. Here we review the current state of studies into this important pathogen/microbiota/host interaction in the mammalian gastrointestinal tract.