The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross-sectional studies. However, there is a lack of studies using prospectively collected samples.
...From the Norwegian Colorectal Cancer Prevention (NORCCAP) trial, we analyzed 144 archived fecal samples from participants who were diagnosed with CRC or high-risk adenoma (HRA) at screening and from participants who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all the samples and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity and differential abundance.
Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls.
was more abundant in CRC compared with healthy controls in both the 16S and metagenome data. The abundance of
and
spp. was associated with time to CRC diagnosis.
Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.
While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the ...intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point.
A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected.
A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the individual and common core microbiota in healthy adults. The findings provide new approaches to define intestinal health and to further characterize the microbial communities inhabiting the human gut.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Blastocystis is an enteric protist and one of the most frequently reported parasitic infections in humans and a variety of animal hosts. It has also been reported in numerous parasite surveys of ...animals in zoological gardens and in particular in non-human primate species. PCR-based methods capable of the direct detection of
Blastocystis in faeces were used to detect
Blastocystis from various hosts, including non-human primates, Australian native fauna, elephants and giraffes, as well as their keepers from a Western Australian zoo. Additional faecal samples were also collected from elephants and giraffes from four other zoos in Amsterdam (The Netherlands), Antwerp (Belgium), Melbourne and Werribee (Australia). Information regarding the general health and lifestyle of the human volunteers were obtained by questionnaire. Overall, 42% and 63% of animals and zoo-keepers sampled from the Western Australian zoo were positive for
Blastocystis, respectively. The occurrence of
Blastocystis in elephants and giraffes from other cities was similar. This is the first report of
Blastocystis found in the elephant, giraffe, quokka, southern hairy nosed wombat and western grey kangaroo. Three novel and what appear to be highly host-specific subtypes (STs) of
Blastocystis in the elephant, giraffe and quokka are also described. These findings indicate that further exploration of the genetic diversity of
Blastocystis is crucial. Most zoo-keepers at the Perth Zoo were harbouring
Blastocystis. Four of these zoo-keeper isolates were identical to the isolates from the southern hairy nosed wombat and five primate species.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Competition with livestock over forage resources has been identified as a potential threat to the survival of the African wild ass (Equus africanus) in the Danakil ecosystem (Eritrea). The Messir ...Plateau is an important breeding area for the African wild ass but also hosts cattle, sheep, goats, donkeys, and camels. Locations and fecal samples of African wild ass and livestock were collected in dry and rainfall months. Stable carbon isotopes δ13C ‰ in fecal samples were used to assess diet composition and overlaps with domestic herbivores. Fecal samples also were used to assess the nutritional quality of African wild ass and domestic donkey diets. During the dry months, African wild ass were concentrated in the northern section of the Messir Plateau, approximately 9 km from the permanent water source, and overlapped spatially with local livestock. During the rainfall months, African wild ass dispersed throughout the Messir Plateau (124 km2) when a high number of livestock, particularly cattle from the highlands with herders, were concentrated in the northern section. During the rainfall months, the northern section had relatively better vegetation cover and access to seasonal water. The grass contribution to the diet of the African wild ass in both dry and rainfall months overlapped significantly with that of domestic donkeys and cattle. In rainfall months, the percent fecal nitrogen and phosphorus contents of African wild ass were significantly lower than those of domestic donkey samples. The lower nutrient levels in fecal samples of African wild ass during rainfall months may be due to their displacement from the northern sector by the high number of immigrant highland cattle with people. Our work provides evidence as to how the presence of domestic herbivores, particularly cattle, may negatively impact the nutrient level of wild equids and threaten the survival of the critically endangered African wild ass.
Captivity maybe the only choice for survival of many endangered vertebrates, and understanding its broad effects is important for animal management and conservation, including breeding endangered ...species for subsequent release. Extreme environmental changes during captivity may influence survival ability in the wild. Captivity decreases gut bacterial diversity in a wide range of animals. However, most studies directly compare animals living in captivity with those in the wild, and there is a lack of understanding of effects of gradient shift in lifestyle during species reintroduction based on the soft-release strategy, which involves a confinement period in a field enclosure. Here, we used 16S rRNA amplicon sequencing to analyze gut microbiomes of 11 captive and 12 semi-wild Przewalski's horses (PH;
) under the same captivity environment, using fecal samples. A subset of samples with abundant extracted DNA (including 3 captive and 3 semi-wild individuals) was selected for whole-genome shotgun sequencing. We found that community diversity did not differ between the semi-wild PH and captive PH, but the semi-wild PH had significantly higher bacterial richness than those in captivity. Relative abundances of all dominant phyla were similar across the semi-wild or captive horses, while those of the non-dominant phyla Tenericutes and Proteobacteria were significantly higher in semi-wild PH than in captive PH. Beta diversity results indicated that bacterial communities of captives and semi-wild horses were clearly separated distinct when considering only composition. Functional profiling of the microbiomes revealed that the semi-wild and captive gut microbiomes were largely similar. However, semi-wild horse microbiomes had higher abundance of bacterial genes related to core metabolic processes, such as carbohydrates, amino acids, and nucleic acid metabolism. The study revealed that semi-wild PH could retain specific non-dominant bacteria and harbor a more diverse microbiome than the captive counterpart, and thus have higher metabolic potential to utilize the complex plants efficiently. These results indicate that change in host lifestyle may play a role in microbiome differentiation in the process of reintroduction, suggesting that a short period of time in captivity is acceptable for PH from the perspective of maintaining the richness of intestinal bacterial flora to some extent.
Fluorescence in situ hybridization and real-time PCR analysis targeting the 16S rRNA gene of Akkermansia muciniphila were performed to determine its presence in the human intestinal tract. These ...techniques revealed that an A. muciniphila-like bacterium is a common member of the human intestinal tract and that its colonization starts in early life and develops within a year to a level close to that observed in adults (10⁸ cells/g) but decreases (P < 0.05) in the elderly.
Pneumonia is the leading cause of morbidity and mortality in children under five years of age worldwide. Over the past decades, studies have shown that the upper respiratory pathogens are closely ...related to the occurrence of pneumonia. However, the co-occurrence of gut microbiome dysbiosis may have clinical manifestation in the prognosis of childhood pneumonia. The aim of the present study is to investigate the differences in gut microbial communities between children's diagnosed community-acquired pneumonia (CAP) under five compared to healthy controls in Inner Mongolia. Fecal samples were collected from children with CAP and healthy controls (<5 years old) and the genomic microbiome 16S rRNA was amplified using the hypervariable V4 region and subjected to MiSeq Illumina sequencing, and then analyzed for microbiota composition and phenotype. Finally functional profiling was performed by KEGG pathways analyses. Our results revealed a gut microbiota dysbiosis in children with CAP. Distinct gut microbiome composition and structure were associated with childhood CAP between two age categories compared to healthy controls. In addition, the phylogenic phenotype's prediction was found to be significantly different between the groups. The prominent genera in age group of 0–3 were Bifidobacterium and Enterococcus. On the contrary, Escherichia-Shigella, Prevotella, Faecalibacterium and Enterobacter were remarkably decreased in most of the fecal samples from CAP patients in age group of 0–3 compared to the control. At the genus level, the CAP children in the age group of 4-5 showed an increase in the abundance of Escherichia/Shigella, Bifidobacterium, Streptococcus and Psychrobacter and, a decrease in the abundance of Faecalibacterium, Bacteroides, Lachnospiraceae and Ruminococcus compared with the matched healthy controls. Moreover, CAP children in both age groups exhibited distinct profiles in the KEGG functional analysis. Our data revealed that the gut microbiota differ between CAP patients and health children and certain gut microbial species are associated with CAP. Further research to identify specific microbial species which may contribute to the development CAP are merited. In addition, rectification of microbiota dysbiosis may provide supplemental benefits for treatment of the childhood CAP.
•Gut microbiota dysbiosis in children with community-acquired pneumonia.•Proteobacteria, was prominent in most of the pneumonia samples of 0–3 y age.•Firmicutes and Bacteroidetes were the most dominant phyla in pneumonia patients of 4–5 years of age.•The phylogenic phenotype's prediction found to be significantly different between the groups.•Pneumonia patients exhibited distinct profiles in the KEGG functional analysis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The probiotic market is increasing world-wide as well as the number of products marketed as probiotics. Among the latter, many products contain
strains at several dosages. However, the scientific ...evidence that should support the probiotic status of those
strains is often contradictory. This review analyses the scientific literature aimed to assess the ability of
strains to survive the human gastrointestinal tract by discussing the scientific validity of the methods applied for the bacterial recovery and identification from stool samples. This review highlights that in most of the intervention studies reviewed, the identification of
strains from stools was not carried out with the necessary taxonomic accuracy to avoid their misidentification with
, a common human commensal and a species phylogenetically close to
. Moreover, this review highlights how critical the accurate taxonomic identification of
in metagenomics-based studies can be.
Ceratonia siliqua, known as the carob, is considered to be of high nutritional value and of great economic significance due to its unique composition. The beneficial effects of carob against cancer, ...metabolic syndrome, diabetes, diarrhea, hyperlipidemia and gastro esophageal reflux disease are only a few of its therapeutic actions. Metabolomics-based analysis provides an ultimate tool, for the deciphering of nutritional intervention derived metabolic alterations. In the present study, 16 male Wistar rats were treated with carob powder for a 15-day period. Fecal and urine samples were collected at 5 time points (0, 1, 5, 10 and 15 days). By the applied HILIC-MS/MS method, 63 and 67 hydrophilic metabolites were detected in the fecal and urine samples, respectively, including amino acids, organic acids, sugars, vitamins and other endogenous compounds. A clear group separation based on fecal metabolome was observed after 1 day and 15 days treatment, while only a mild differentiation at day 1 was observed based on urine metabolome. Twenty-one fecal metabolites were responsible for the separation including amino acids and their derivatives, vitamins and organic acids. However, only 7 metabolites were altered in rat urine samples. Metabolic alterations in fecal samples could be attributed to physiological and biochemical adaptations derived from the nutritional intervention. Fecal targeted metabolomics were proven to be suitable for uplifting and highlighting such alterations.
•Carob is considered to be a functional food with high nutritional value (both for humans and animals).•Wistar rats were fed with carob powder diluted in water (15 days) for foodomics examination.•A selected panel of metabolites could provide urine and fecal biomarkers of nutritional habits.•HILIC-MS/MS reveals significantly altered amino acids patterns in carob treated rats.•Compared to urine, fecal metabolome was found more susceptible in carob treatment.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study assesses the clinical relevance of dipeptidyl peptidase 4 (DPP4) membrane exopeptidase as a biomarker of inflammatory bowel disease (IBD). A spike-and-recovery approach of DPP4 in fecal ...samples was used to compare two different methods for protein extraction, followed by a stability assessment.
Fecal samples of healthy volunteers spiked with known concentrations of recombinant DPP4 were processed using a standard manual extraction protocol and the CALEX
protocol. The two methods were compared by quantification of fecal DPP4 by ELISA, followed by Bland-Altman analysis. For the stability assays DPP4 was extracted from fecal samples and stored under different conditions of temperature and time after collection.
In general, the levels of spiked DPP4 in stool samples were lower with the manual protocol than in those obtained with the CALEX
method; this trend was corroborated by Bland-Altman analysis. Nonetheless, variability was within the acceptable limits for both protocols. In the stability assessment, no statistically significant differences were found between the results obtained under the different storage conditions.
Both manual and CALEX
protocols provided equal extraction ability of DPP4 from stool samples. In addition, DPP4 provided flexibility in terms of sample storage enabling the accurate assessment of samples delivered up to a week before analysis.
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