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Cancer Management and Research 2020Besides genetic and epigenetic alterations that lead to carcinogenesis and development of colorectal cancer (CRC), intestinal microbiomes are recently recognized to play...
INTRODUCTION
Besides genetic and epigenetic alterations that lead to carcinogenesis and development of colorectal cancer (CRC), intestinal microbiomes are recently recognized to play a critical role in CRC progression. The abundant species associated with human CRC have been proposed for their roles in promoting tumorigenesis. However, a recent "driver-passenger" model suggests that these CRC-associated species with high relative abundances may be passenger bacteria that take advantage of the tumor environment instead of initiating CRC, whereas the driver species that initiate CRC have been replaced by passenger bacteria due to the alteration of the intestinal niche.
METHODS
Here, to reveal potential driver and passenger bacteria during CRC progression, we compare the gut mucosal microbiomes of 75 triplet-paired CRC samples collected from on-tumor site, adjacent-tumor site, and off-tumor site, and 26 healthy controls.
RESULTS
Our analyses revealed potential driver bacteria in four genera and two families, and potential passenger bacteria in 14 genera or families. and were predicted to be potential driver bacteria. Moreover, 14 potential passenger bacteria were identified and divided into five groups. Group I passenger bacteria contain , and . Group II passenger bacteria contain . Group III passenger bacteria contain . Group IV passenger bacteria contain , and . Group V passenger bacteria contain . Co-occurrence network analysis reveals a low correlation relationship between driver and passenger bacteria in CRC patients compared with healthy controls.
DISCUSSION
These driver and passenger species may serve as bio-marker species for screening cohorts with high risk to initiate CRC or patients with CRC, respectively. Further functional studies will help understand the roles of driver and passenger bacteria in CRC initiation and development.
PubMed: 33209059
DOI: 10.2147/CMAR.S275316 -
Pediatric Research Jul 2021Patients following repair of an esophageal atresia (EA) or tracheoesophageal fistula (TEF) carry an increased risk of long-term cardiopulmonary malaise. The role of the...
BACKGROUND
Patients following repair of an esophageal atresia (EA) or tracheoesophageal fistula (TEF) carry an increased risk of long-term cardiopulmonary malaise. The role of the airway microbiome in EA/TEF patients remains unclear.
METHODS
All EA/TEF patients treated between 1980 and 2010 were invited to a prospective clinical examination, spirometry, and spiroergometry. The airway microbiome was determined from deep induced sputum by 16 S rRNA gene sequencing. The results were compared to a healthy age- and sex-matched control group.
RESULTS
Nineteen EA/TEF patients with a mean age of 24.7 ± 7 years and 19 age- and sex-matched controls were included. EA/TEF patients showed a significantly lower muscle mass, lower maximum vital capacity (VC), and higher rates of restrictive ventilation disorders. Spiroergometry revealed a significantly lower relative performance capacity and lower peak VO in EA/TEF patients. Alpha- and beta-diversity of the airway microbiome did not differ significantly between the two groups. Linear discriminant effect size analysis revealed significantly enriched species of Prevotella_uncultured, Streptococcus_anginosus, Prevotella_7_Prevotella_enoeca, and Mogibacterium_timidum.
CONCLUSION
EA/TEF patients frequently suffer from restrictive ventilation disorders and impaired cardiopulmonary function associated with minor alterations of the airway microbiome. Long-term examinations of EA/TEF patients seem to be necessary in order to detect impaired cardiopulmonary function.
IMPACT
The key messages of the present study are a significantly decreased VC and exercise performance, as well as airway microbiome differences in EA/TEF patients. This study is the first to present parameters of lung function and exercise performance in combination with airway microbiome analysis with a mean follow-up of 24 years in EA/TEF patients. Prospective, long-term studies are needed to unravel possible interactions between alterations of the airway microbiome and impaired pulmonary function in EA/TEF patients.
Topics: Adult; Case-Control Studies; Esophageal Atresia; Female; Humans; Male; Microbiota; Prospective Studies; Young Adult
PubMed: 33159185
DOI: 10.1038/s41390-020-01222-7 -
BMC Oral Health Oct 2020Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to...
BACKGROUND
Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in 6-8 years old children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.
METHODS
Children 6 to 8 years old living in rural isolated areas including 40 caries-active subjects and 40 caries-free subjects were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ) technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.
RESULTS
We found 6 phyla and 13 genera predominant in all the samples, and differences in relative abundances can be observed. The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P < 0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P < 0.05). The core microbiome was defined as 18 predominant genera in children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups.
CONCLUSIONS
The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for children with caries. In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.
Topics: Aged; Child; Chromatography, Liquid; Dental Caries; Humans; Microbiota; RNA, Ribosomal, 16S; Saliva; Salivary Proteins and Peptides; Tandem Mass Spectrometry
PubMed: 33115458
DOI: 10.1186/s12903-020-01262-9 -
Frontiers in Microbiology 2020The aim of the study was to investigate the effect of untreated and processed rapeseed meal (RSM) on fiber degradability by pig gut microbiota and the adaptation of the...
The aim of the study was to investigate the effect of untreated and processed rapeseed meal (RSM) on fiber degradability by pig gut microbiota and the adaptation of the microbiota to the substrate, by using the Swine Large Intestine Model (SLIM). A standardized swine gut microbiota was fed for 48 h with pre-digested RSM which was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. Amplicons of the V3-V4 region of the 16S rRNA gene were sequenced to evaluate the gut microbiota composition, whereas short chain fatty acids (SCFA) were measured to assess fiber degradation. Adaptive gPCA showed that CELL and ALK had larger effects on the microbiota composition than PECT1 and PECT2, and all substrates had larger effects than CON. The relative abundance of family Prevotellaceae was significantly higher in CELL treatment compared to other treatments. Regardless of the treatments (including CON), the relative abundance of , , and (in the order of Clostridiales) were significantly increased after 24 h, and , , , , 009, , , and were significantly higher in abundance at time point 48 compared to the earlier time points. 9 had significant positive correlations with propionic and valeric acid, and positively correlated with acetic and caproic acid. There was no significant difference in SCFA production between untreated and processed RSM. Overall, degradability in the processed RSM was not improved compared to CON. However, the significantly different microbes detected among treatments, and the bacteria considerably correlating with SCFA production might be important findings to determine strategies to shorten the fiber adaptation period of the microbiota, in order to increase feed efficiency in the animal, and particularly in pig production.
PubMed: 32983078
DOI: 10.3389/fmicb.2020.570985 -
PeerJ 2020The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible...
BACKGROUND
The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ.
METHODS
In this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity.
RESULTS
The alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo- =3.337, < 0.001, uncorrected). At the phylum level, relatively more and less ( < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of , , , , , undefined and undefined were significantly increased, whereas the abundances of , , and were decreased in the SZ group compared to the NC group ( < 0.05, FDR corrected). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between the two groups, including the Polyketide sugar unit biosynthesis, Valine, Leucine and Isoleucine biosynthesis, Pantothenate and CoA biosynthesis, C5-Branched dibasic acid metabolism, Phenylpropanoid biosynthesis, Ascorbate and aldarate metabolism, Nucleotide metabolism and Propanoate metabolism pathways ( < 0.05, FDR corrected). Among the SZ group, the abundance of was positively correlated with the total Positive and Negative Syndrome Scale (PANSS) scores ( = 0.24, < 0.05, uncorrected) as well as the general PANSS scores ( = 0.22, < 0.05, uncorrected); was negatively related to the negative scores of PANSS ( = 0.22, < 0.05, uncorrected).
CONCLUSIONS
Our findings provided evidence of altered gut microbial composition in SZ group. In addition, we found that and were associated with the severity of symptoms for the first time, which may provide some new biomarkers for the diagnosis of SZ.
PubMed: 32821537
DOI: 10.7717/peerj.9574 -
Biology of Blood and Marrow... Nov 2020Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide...
Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide colonization resistance against dominance of potential pathogens, and GM dysbiosis following HCT can be deleterious to immune reconstitution. Little is known about the composition, diversity, and evolution of GM communities in HCT patients and their association with subsequent febrile neutropenia (FN) and infection. Identification of markers before HCT that predict subsequent infection could be useful in developing individualized antimicrobial strategies. Fecal samples were collected prospectively from 33 HCT recipients at serial time points: baseline, post-conditioning regimen, neutropenia onset, FN onset (if present), and hematologic recovery. GM was assessed by 16S rRNA sequencing. FN and major infections (ie, bloodstream infection, typhlitis, invasive fungal infection, pneumonia, and Clostridium difficile enterocolitis) were identified. Significant shifts in GM composition and diversity were observed during HCT, with the largest alterations occurring after initiation of antibiotics. Loss of diversity persisted without a return to baseline at hematologic recovery. GM in patients with FN was enriched in Mogibacterium, Bacteroides fragilis, and Parabacteroides distasonis, whereas increased abundance of Prevotella, Ruminococcus, Dorea, Blautia, and Collinsella was observed in patients without fever. A baseline protective GM profile (BPGMP) was predictive of protection from major infection. The BPGMP was associated with subsequent major infections with 77% accuracy and an area under the curve of 79%, with sensitivity, specificity, and positive and negative predictive values of 0.71, 0.91, 0.77, and 0.87, respectively. Our data show that large shifts in GM composition occur early after HCT, and differences in baseline GM composition are associated with the development of subsequent major infections.
Topics: Bacteroidetes; Feces; Gastrointestinal Microbiome; Hematopoietic Stem Cell Transplantation; Humans; RNA, Ribosomal, 16S
PubMed: 32717434
DOI: 10.1016/j.bbmt.2020.07.023 -
Microorganisms Jun 2020To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial...
To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial communities that prevail in this population. To this end, we profiled the faecal bacterial community of 140 Indonesian schoolchildren in urban Makassar. The core microbiota of Indonesian schoolchildren consisted of , , and multiple members of the and families, but the relative abundance of these taxa varied greatly among children. Socioeconomic status (SES) was the main driver for differences in microbiota composition. Multiple bacterial genera were differentially abundant between high and low SES children, including , and . In addition, the microbiota of high SES children was less diverse and strongly associated with body mass index (BMI). In low SES children, helminth infection was prevalent and positively associated with , and abundance, while negatively associated with relative abundance of . Protozoa infection was also prevalent, and positively associated with while it was negatively associated with the relative abundance of and . In conclusion, Indonesian schoolchildren living in urban Makassar share a core microbiota, but their microbiota varies in diversity and relative abundance of specific bacterial taxa depending on socioeconomic status, nutritional status, and intestinal parasites infection.
PubMed: 32604882
DOI: 10.3390/microorganisms8060961 -
Annals of Surgical Oncology Feb 2021Subtotal gastrectomy with Billroth II reconstruction (SGB2) results in increased gastric pH and diminished gastric barrier. Increased gastric pH following PPI therapy...
BACKGROUND
Subtotal gastrectomy with Billroth II reconstruction (SGB2) results in increased gastric pH and diminished gastric barrier. Increased gastric pH following PPI therapy has an impact on the gut microbiome, intestinal inflammation, and possibly patient health. If similar changes are present after SGB2, these can be relevant for patient health and long-term outcomes after surgery. The aim of the study is to investigate whether SGB2 is associated with specific changes in gut microbiome composition and intestinal inflammation.
PATIENTS AND METHODS
This cross-sectional proof-of-concept study includes patients after SGB2 (n = 14) for early gastric cancer and their nongastrectomized in-house relatives as controls (n = 8). Fecal microbiome composition, intestinal inflammation (fecal calprotectin), gut permeability (DAO, LBP, sCD14), systemic inflammation (CRP) markers, and gastrointestinal symptoms are investigated. This study is registered at ClinicalTrials.gov (NCT03418428).
RESULTS
Microbiome oralization following SGB2 was defined by an increase in Escherichia-Shigella, Enterococcus, Streptococcus, and other typical oral cavity bacteria (Veillonella, Oribacterium, and Mogibacterium) abundance. The fecal calprotectin was increased in the SGB2 group [100.9 (52.1; 292) vs. 25.8 (17; 66.5); p = 0.014], and calprotectin levels positively correlated with the abundance of Streptococcus (r = 0.639; p = 0.023). Gastrointestinal symptoms in SGB2 patients were associated with distinct taxonomic changes of the gut microbiome.
CONCLUSIONS
SGB2 is associated with oralization of the gut microbiome; intestinal inflammation and microbiome changes were associated with gastrointestinal symptoms. These novel findings may open gut microbiome as a new target for therapy to improve quality of life and general patient health in long-term survivors after SGB2.
Topics: Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Cross-Sectional Studies; Female; Gastrectomy; Gastroenterostomy; Gastrointestinal Microbiome; Humans; Inflammation; Male; Quality of Life
PubMed: 32504369
DOI: 10.1245/s10434-020-08678-1 -
Animals : An Open Access Journal From... May 2020The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the...
The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. Twenty-six Nubian healthy female goats were selected as experimental animals, and their TDC was determined using metabolic experiments. Eight goats were grouped into the high digestibility of Calcium (HC) phenotype, and another eight were grouped into the low digestibility of Calcium (LC) phenotype. Their bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum, and colon contents were sequenced using next-generation high-throughput sequencing technology. In the rumen, 239 genera belonging to 23 phyla, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected. In addition, there was a significant correlation between the TDC and the relative abundance of , _-7_, , 1, _004, _2, in the rumen, , 3007_, 3201088-5_, and in the abomasum, in the cecum, and in the cecum were observed. This study suggests an association of GIT microbial communities as a factor influencing TDC in goats.
PubMed: 32443450
DOI: 10.3390/ani10050875 -
Journal of Dairy Science Apr 2020Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important...
Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition from otherwise host-inaccessible dietary components. The rumen environment is noted for its substantial spatial heterogeneity, as illustrated by the stratification into ruminal solid and liquid phases. A third microbiota found directly attached to the ruminal epithelium (the epimural microbiota) also exists but is less well understood because of challenges in sampling the ruminal epithelium. As a result, our understanding of the epimural microbiota is based on analyses of cannulated animals sampled at a single location-the ventral sac-and does not account for other ruminal locations, which may have importance for overall rumen function. To address this knowledge gap, we hypothesize that the epimural microbiota at different ruminal locations differs due to known morphological, physiological, and functional differences across the geographic spread of the rumen epithelium. Here, we characterized bacterial epimural communities at different sites within 8 lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy: cranial sac (CS), ventral sac (VS), caudodorsal blind sac (CDBS), and caudoventral blind sac (CVBS). We found that locations differed in both epimural bacterial community structure and composition, with the CDBS community displaying the greatest diversity. Across all sampling sites, epimural bacterial communities were dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high relative sequence abundance and differential distributions according to sample location. There appears to be a core epimural microbiota present across all locations in all cows, although relative abundance was highly variable. The difference in relative abundance in epimural microbial communities, perhaps influenced by host physiology and the diversity within rumen contents, likely has important consequences for nutrition acquisition and general health. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.
Topics: Animals; Bacteria; Biodiversity; Cattle; Diet; Female; Lactation; Microbiota; RNA, Ribosomal, 16S; Rumen
PubMed: 32057427
DOI: 10.3168/jds.2019-17649