scholarly journals CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

2019 ◽  
Author(s):  
Maxime Borry ◽  
Bryan Cordova ◽  
Angela Perri ◽  
Marsha C. Wibowo ◽  
Tanvi Honap ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dna Content ◽  
Fecal Material ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
The Past ◽  
Microscopic Features ◽  
Archaeological Sediments ◽  
Microbial Dna

ABSTRACTShotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

scholarly journals CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9001 ◽  
Author(s):  
Maxime Borry ◽  
Bryan Cordova ◽  
Angela Perri ◽  
Marsha Wibowo ◽  
Tanvi Prasad Honap ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dna Content ◽  
Fecal Material ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
The Past ◽  
Microscopic Features ◽  
Archaeological Sediments ◽  
Microbial Dna

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

scholarly journals Shotgun metagenomics reveals significant gut microbiome features in different grades of acute pancreatitis

2020 ◽  
Author(s):  
Shanshan Yu ◽  
Yangyang Xiong ◽  
Yangyang Fu ◽  
Guorong Chen ◽  
Huadong Zhu ◽  
...  
Keyword(s):  
Acute Pancreatitis ◽  
Gut Microbiota ◽  
Severe Acute Pancreatitis ◽  
Gut Microbiome ◽  
Glutathione Metabolism ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
Considerable Morbidity ◽  
Mild Acute Pancreatitis ◽  
And Function

Abstract Background: Acute pancreatitis (AP) has a broad spectrum of severity and is associated with considerable morbidity and mortality. We aimed to evaluate the composition and functional effects of gut microbiota in different grades of AP severity. Results: Gut microbiota in AP patients was characterized by decreased species richness. The most representative gut microbiota in mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP), and severe acute pancreatitis (SAP) was Streptococcus, Escherichia-coli, and Enterococcus, respectively. Each of the three AP-associated genera could differentiate AP from healthy control population. Representative pathways associated with the glutathione metabolism, lipopolysaccharide biosynthesis, and amino acid metabolism (valine, leucine and isoleucine degradation) were enriched in MAP, MSAP, and SAP, respectively. Conclusions: Our findings indicate that in patients with AP, the gut microbiome composition and function are correlated with different severity of AP from a whole-genome perspective, and new changes are observed.

scholarly journals Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients

2021 ◽  
Author(s):  
Yueqiong Ni ◽  
Zoltan Lohinai ◽  
Yoshitaro Heshiki ◽  
Balazs Dome ◽  
Judit Moldvay ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Gut Microbiota ◽  
Cancer Patients ◽  
Gut Microbiome ◽  
Human Gut ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Lung Cancer Patients ◽  
Microbial Species ◽  
Functional Pathways

AbstractCachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.

scholarly journals Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Ce Yuan ◽  
Michael B. Burns ◽  
Subbaya Subramanian ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Mirna Expression ◽  
Gut Microbiome ◽  
Noncoding Rna ◽  
Microbial Community Composition ◽  
Host Cells ◽  
Microbiome Composition ◽  
Small Noncoding Rna

ABSTRACT Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes , Bacteroidetes , and Proteobacteria . Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Successional stages in infant gut microbiota maturation

2021 ◽  
Author(s):  
Leen Beller ◽  
Ward Deboutte ◽  
Gwen Falony ◽  
Sara Vieira Silva ◽  
Raul Tito ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Early Life ◽  
Microbial Colonization ◽  
Maturation Stage ◽  
Gut Flora ◽  
Microbiome Composition ◽  
Gut Colonization ◽  
Maturation Stages ◽  
Colonization Process ◽  
First Year Of Life

Background: Disturbances in the primary colonization of the infant gut can result in life-long consequences and have been associated with a range of host conditions. Although early life factors have been shown to affect the infant gut microbiota development, our current understanding of the human gut colonization in early life remains limited. To gain more insights in the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (total number of samples, n=303). To evaluate gut microbiota maturation transition towards an adult configuration, we compared the microbiome composition of the infants to the Flemish Gut Flora Project population (n=1,106). Results: We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the Flemish Gut Flora Project (FGFP) cohort clustered all infant samples within the (in adults) potentially dysbiotic Bact2 enterotype. Conclusion: We confirmed similarities between infant gut microbial colonization and adult dysbiosis. A profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.

scholarly journals Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
T. Goolam Mahomed ◽  
R. P. H. Peters ◽  
M. Allam ◽  
A. Ismail ◽  
S. Mtshali ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Small Sample ◽  
Chronic Obstructive ◽  
Shotgun Metagenomics ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition ◽  
Disease States ◽  
Dna And Rna ◽  
Lung Microbiome ◽  
Copd Patients

AbstractChronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

Underdevelopment of the gut microbiota and bacteria species as non-invasive markers of prediction in children with autism spectrum disorder

Gut ◽  
2021 ◽  
pp. gutjnl-2020-324015
Author(s):  
Yating Wan ◽  
Tao Zuo ◽  
Zhilu Xu ◽  
Fen Zhang ◽  
Hui Zhan ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Chinese Children ◽  
Chronological Age ◽  
Microbiome Composition ◽  
Children With Asd ◽  
Faecal Microbiome

ObjectiveThe gut microbiota has been suggested to play a role in autism spectrum disorder (ASD). We postulate that children with ASD harbour an altered developmental profile of the gut microbiota distinct from that of typically developing (TD) children. Here, we aimed to characterise compositional and functional alterations in gut microbiome in association with age in children with ASD and to identify novel faecal bacterial markers for predicting ASD.DesignWe performed deep metagenomic sequencing in faecal samples of 146 Chinese children (72 ASD and 74 TD children). We compared gut microbial composition and functions between children with ASD and TD children. Candidate bacteria markers were identified and validated by metagenomic analysis. Gut microbiota development in relation to chronological age was assessed using random forest model.ResultsASD and chronological age had the most significant and largest impacts on children’s faecal microbiome while diet showed no correlation. Children with ASD had significant alterations in faecal microbiome composition compared with TD children characterised by increased bacterial richness (p=0.021) and altered microbiome composition (p<0.05). Five bacterial species were identified to distinguish gut microbes in ASD and TD children, with areas under the receiver operating curve (AUC) of 82.6% and 76.2% in the discovery cohort and validation cohort, respectively. Multiple neurotransmitter biosynthesis related pathways in the gut microbiome were depleted in children with ASD compared with TD children (p<0.05). Developing dynamics of growth-associated gut bacteria (age-discriminatory species) seen in TD children were lost in children with ASD across the early-life age spectrum.ConclusionsGut microbiome in Chinese children with ASD was altered in composition, ecological network and functionality compared with TD children. We identified novel bacterial markers for prediction of ASD and demonstrated persistent underdevelopment of the gut microbiota in children with ASD which lagged behind their respective age-matched peers.

scholarly journals Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Debra Poutsiaka ◽  
Lori Stern ◽  
Virginia Riquelme ◽  
Emily Hollister ◽  
Julia Cope ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Lactobacillus Rhamnosus ◽  
Detailed Examination ◽  
Global Changes ◽  
Shotgun Metagenomics ◽  
Gene Abundance ◽  
Funding Sources ◽  
And Function ◽  
Relative Gene

Abstract Objectives This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI. Methods Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group). Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes. Results Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25. Conclusions We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI. Funding Sources Pfizer Inc.

The link between autism spectrum disorder and gut microbiota: A scoping review

Autism ◽  
2020 ◽  
Vol 24 (6) ◽  
pp. 1328-1344 ◽  
Author(s):  
Amanda Nitschke ◽  
Raywat Deonandan ◽  
Anne TM Konkle
Keyword(s):  
Autism Spectrum Disorder ◽  
Gut Microbiota ◽  
Scoping Review ◽  
Bacterial Species ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Exclusion Criteria ◽  
The Past ◽  
Gastrointestinal Distress ◽  
Special Diets

Gut dysfunction and microbial dysbiosis comorbidities are of particular interest in recent autism research, as gastrointestinal distress is present in up to 90% of autism spectrum disorder cases and therefore may play a key role in the pathogenesis of this disorder. This scoping review aims to integrate the results of studies conducted in the past 6 years examining the association between gut microbiota and autism spectrum disorder, specifically with regard to the characterization of autism spectrum disorder microbiota and potential therapeutic interventions. Studies related to the gastrointestinal microbiome of subjects with autism spectrum disorder were identified through PubMed, SCOPUS, PsycInfo, and Google Scholar databases. Studies were screened and selected based on defined inclusion and exclusion criteria; 19 studies were included. Research continues to report differences between microbiota of individuals with autism spectrum disorder and controls; however, the types and abundances of bacteria present remain inconsistent. Promising treatment interventions for autism spectrum disorder, including special diets, dietary supplementation, and of particular interest, microbiota transfer therapy, are also being explored. Research regarding the link between gut microbiota and autism spectrum disorder renders exciting results; however, it is still in its infancy of investigation. Rigorous methodologies are required to support and strengthen the reliability of existing results, and to further our understanding of the pathogenesis of autism spectrum disorder. Lay abstract Gastrointestinal distress and gut microbial imbalances are commonly found in children with autism spectrum disorder, and therefore may play a key role in the development of the disorder. This scoping review aimed to examine the extent, range and nature of research conducted in the past 6 years that focused on furthering our understanding of autism spectrum disorder and its association with gut microbiota. A literature review was performed with predetermined key words. Studies were screened and selected based on defined inclusion and exclusion criteria. A total of 19 studies were included for final analysis. While there are continuous reports of differences in gut microbiota between autism spectrum disorder and neurotypical individuals, knowledge about the consistency in the presence and abundance of bacterial species, as well as metabolites, remains deficient. Treatments such as special diets, vitamin, prebiotic, probiotic, and microbiota transfer therapy show promising therapeutic potential, yet are in their infancy of investigation. Overall, further research with rigorous methodologies is required to support and strengthen the reliability of existing findings. Future research should aim to increase sample sizes, eliminate biases, and subgroup autism spectrum disorder groups to help accommodate for inter-individual variation. As increasing evidence of a unique autism spectrum disorder microbiome and metabolome is acquired, autism spectrum disorder-specific biomarkers can be identified. These biomarkers have great implications in terms of elucidating the molecular mechanisms of autism spectrum disorder, preventing the onset of autism spectrum disorder, and improving treatments for individuals with autism spectrum disorder.

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