Impact of COVID-19 on the Intestinal Microbiome

In order to understand the structure and dynamics of symbiotic relationships of human intestinal biotope micro-organisms, taxonomic constancy indices, the degree of contagion of the biocenosis under study and floristic significance were investigated, which made it possible to detect qualitative and quantitative changes in the microecology of the biotope being studied in persons living in different ecologically heterogeneous territories of Saint Petersburg. The contagiosity index estimated the distribution of species in space. Persons living in the ecologically disadvantaged Kirov district of the city have been found to show a reliable increase in this indicator for the obligate microflora: bifido and lacto bacteria, intestinal columns and bacteroids, compared to the resort district, which is considered a relatively favourable area for residence. On the contrary, there has been a reliable decrease in this indicator in the group of opportunistic micro-organisms (fungi of the genus Candida, staphylococcus, clostridium, etc.), resulting in the liberation of ecological niches successfully occupied by transient flora. This ratio reveals an imbalance of participation in the horizontal structure of the intestine ecosystem of the main symbiotes and representatives of the transient flora. To analyse the structure of symbiotic relationships, the constancy indices that form the microflora of the individuals of the groups studied were investigated. The analysis of the data obtained suggested that the dominant species in both groups were optional-anaerobic bifido and lactobacteria and oblique-anaerobic bacteroids. It should be noted, however, that in the residents of the dysfunctional Kirovsky district, against the background of the reduced constancy of the normal flora, opportunistic micro-organisms have entered. The floral significance index was also declining in the obligate flora of this group and increased for opportunistic species. Thus, the study of the environmental characteristics of the intestinal biotope using different ecological parameters for persons living in different technogenic load regions of St. Petersburg has shown that in the Kirov district with an unfavourable environmental situation there are compensated qualitative and quantitative changes in the intestinal microbiocenosis, resulting in a change in the hierarchy in the overall structure of micro-organisms.

Download Full-text

Faculty Opinions recommendation of In-feed antibiotic effects on the swine intestinal microbiome.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13765958.15187058 ◽

2012 ◽

Author(s):

Paul Cotter

Keyword(s):

Intestinal Microbiome

Download Full-text

Analysis of the Small Intestinal Microbiome of Children With Autism

10.21236/ada584963 ◽

2013 ◽

Author(s):

Rafail Kushak

Keyword(s):

Children With Autism ◽

Intestinal Microbiome ◽

Small Intestinal

Download Full-text

Analysis of Small Intestinal Microbiome in Children with Autism

10.21236/ada575715 ◽

2013 ◽

Author(s):

Rafail Kushak

Keyword(s):

Children With Autism ◽

Intestinal Microbiome ◽

Small Intestinal

Download Full-text

Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion

Scientific Reports ◽

10.1038/s41598-021-95992-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lama Nazzal ◽

Fritz Francois ◽

Nora Henderson ◽

Menghan Liu ◽

Huilin Li ◽

...

Keyword(s):

Kidney Stones ◽

Stone Formation ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Urinary Oxalate ◽

Treatment Groups ◽

The Us ◽

Urine Electrolytes ◽

H Pylori ◽

Urinary Oxalate Excretion

AbstractThe incidence of kidney stones is increasing in the US population. Oxalate, a major factor for stone formation, is degraded by gut bacteria reducing its intestinal absorption. Intestinal O. formigenes colonization has been associated with a lower risk for recurrent kidney stones in humans. In the current study, we used a clinical trial of the eradication of Helicobacter pylori to assess the effects of an antibiotic course on O. formigenes colonization, urine electrolytes, and the composition of the intestinal microbiome. Of 69 healthy adult subjects recruited, 19 received antibiotics for H. pylori eradication, while 46 were followed as controls. Serial fecal samples were examined for O. formigenes presence and microbiota characteristics. Urine, collected serially fasting and following a standard meal, was tested for oxalate and electrolyte concentrations. O. formigenes prevalence was 50%. Colonization was significantly and persistently suppressed in antibiotic-exposed subjects but remained stable in controls. Urinary pH increased after antibiotics, but urinary oxalate did not differ between the control and treatment groups. In subjects not on antibiotics, the O. formigenes-positive samples had higher alpha-diversity and significantly differed in Beta-diversity from the O. formigenes-negative samples. Specific taxa varied in abundance in relation to urinary oxalate levels. These studies identified significant antibiotic effects on O. formigenes colonization and urinary electrolytes and showed that overall microbiome structure differed in subjects according to O. formigenes presence. Identifying a consortium of bacterial taxa associated with urinary oxalate may provide clues for the primary prevention of kidney stones in healthy adults.

Download Full-text

P60.02 Insight Into Intestinal Microbiome in NSCLC Patients: More Personalized Immunotherapy in the Crosshairs

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2021.01.961 ◽

2021 ◽

Vol 16 (3) ◽

pp. S541

Author(s):

A. Grenda ◽

E. Iwan ◽

P. Krawczyk ◽

M. Słomiany-Szwarc ◽

A. Bomba ◽

...

Keyword(s):

Intestinal Microbiome ◽

Nsclc Patients ◽

Insight Into

Download Full-text

678 Addition of a single bacteria facilitates anti-tumor immunity and long-term survival in colorectal cancer

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0678 ◽

2020 ◽

Vol 8 (Suppl 3) ◽

pp. A717-A717

Author(s):

Abigail Overacre-Delgoffe ◽

Anthony Cillo ◽

Hannah Bumgarner ◽

Ansen Burr ◽

Justin Tometich ◽

...

Keyword(s):

Colorectal Cancer ◽

T Cells ◽

Tumor Immunity ◽

Tumor Burden ◽

Intestinal Microbiome ◽

Tumor Control ◽

Mesenteric Lymph Nodes ◽

Term Survival ◽

16S Sequencing ◽

Tumor Bearing

BackgroundColorectal cancer remains one of the most common and deadliest cancers worldwide and effective therapies are lacking. While immunotherapy has revolutionized treatment for many cancers, the overwhelming majority of colorectal cancer patients are non-responsive and the 5-year survival rate for advanced disease is <20%. Immunotherapeutic response has been associated with select members of the microbiome in melanoma; however, the potential benefit in colorectal cancer and the underlying mechanisms remain unclear. We sought to determine how specific members of the intestinal microbiome affect anti-tumor immunity in colorectal cancer (CRC) in hopes of discovering novel treatments and revealing potential hurdles to current therapeutic response in CRC patients.MethodsWe utilized a carcinogen-induced mouse model of CRC and colonized half of the tumor-bearing mice with Helicobacter hepaticus (Hhep) 7 weeks post AOM. Tumor number was assessed 12 weeks post AOM. We isolated lymphocytes from the lamina propria, colonic epithelium, mesenteric lymph nodes, and tumor(s) to track the spatial and transcriptional Hhep-specific and endogenous immune responses during tumor progression through 5’ single cell RNAseq, flow cytometry, and immunofluorescence. In addition, we utilized 16S sequencing and FISH to track Hhep colonization, location within the colon, and its impact on the surrounding microbiome.ResultsWe have found that rational modification of the microbiome of colon tumor-bearing mice through addition of a single bacteria, Hhep, led to tumor control or clearance and a significant survival advantage. Colonization led to the expansion of the lymphatic network and development of numerous peri- or intra-tumoral tertiary lymphoid structures (TLS) composed of Hhep-specific CD4 T follicular helper cells (TFH) as well as the bacteria itself. This led to an overall ‘heating’ of the tumor, wherein we saw an increase of CD4 T cell infiltration to the tumor core as well as an increase in CD103+ type 1 DC (cDC1) recruitment through increased chemokines such as CCL5 and XCL1. Hhep-specific TFH were both necessary and sufficient to drive TLS formation, increased immune invasion, and anti-tumor immunity.ConclusionsWe have shown that addition of a single bacteria, Hhep, leads to a reduction in CRC tumor burden or clearance through lymphatic expansion, TLS formation, and remodeling of the tumor microenvironment, and that Hhep-specific T cells are required for tumor control. These studies suggest that rational modification of the microbiome and microbiome-specific T cells can positively impact anti-tumor immunity and may represent a unique immunotherapeutic target to turn resistant tumors into responsive tumors.

Download Full-text

Sulpiride Serves, a Substrate for the Gut Microbiome

Dose-Response ◽

10.1177/1559325820987943 ◽

2021 ◽

Vol 19 (1) ◽

pp. 155932582098794

Author(s):

Imran Mukhtar ◽

Haseeb Anwar ◽

Osman Asghar Mirza ◽

Qasim Ali ◽

Muhammad Umar Ijaz ◽

...

Keyword(s):

Oral Administration ◽

Gut Microbiome ◽

Drug Target ◽

Membrane Transporters ◽

Intestinal Microbiome ◽

Albino Rats ◽

Body Organ ◽

Total Absorbance ◽

Research World

In the contemporary research world, the intestinal microbiome is now envisioned as a new body organ. Recently, the gut microbiome represents a new drug target in the gut, since various orthologues of intestinal drug transporters are also found present in the microbiome that lines the small intestine of the host. Owing to this, absorbance of sulpiride by the gut microbiome in an in vivo albino rats model was assessed after the oral administration with a single dose of 20mg/kg b.w. The rats were subsequently sacrificed at 2, 3, 4, 5 and 6 hours post oral administration to collect the gut microbial mass pellet. The drug absorbance by the gut microbiome was determined by pursuing the microbial lysate through RP-HPLC-UV. Total absorbance of sulpiride by the whole gut microbiome and drug absorbance per milligram of microbial pellet were found significantly higher at 4 hours post-administration as compared to all other groups. These results affirm the hypothesis that the structural homology between membrane transporters of the gut microbiome and intestinal epithelium of the host might play an important role in drug absorbance by gut microbes in an in vivo condition.

Download Full-text

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

Download Full-text