Tag: gut flora

Studies find that microbiome changes may be a signature for ME/CFS

Researchers have found differences in the gut microbiomes of people with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) compared to healthy controls. Findings from two studies, published in Cell Host & Microbe and funded by the National Institutes of Health add to growing evidence that connects disruptions in the gut microbiome, the complete collection of bacteria, viruses, and fungi that live in our gastrointestinal system, to ME/CFS.

“The microbiome has emerged as a potential contributor to ME/CFS. These findings provide unique insights into the role the microbiome plays in the disease and suggest that certain differences in gut microbes could serve as biomarkers for ME/CFS,” said Vicky Whittemore, Ph.D., program director at NIH’s National Institute of Neurological Disorders and Stroke (NINDS).

ME/CFS is a serious, chronic, and debilitating disease characterized by a range of symptoms, including fatigue, post-exertional malaise, sleep disturbance, cognitive difficulties, pain, and gastrointestinal issues. The causes of the disease are unknown and there are no treatments.

In one study, senior author Brent L. Williams, Ph.D., assistant professor, W. Ian Lipkin, M.D., John Snow Professor of Epidemiology and director of the Center for Infection and Immunity at the Columbia University Mailman School of Public Health, in New York City, and their collaborators analyzed the genetic makeup of gut bacteria in fecal samples collected from a geographically diverse cohort of 106 people with ME/CFS and 91 healthy controls. The results revealed key differences in microbiome diversity, quantity, metabolic pathways, and interactions between species of gut bacteria.

Dr. Williams and his colleagues found that people with ME/CFS had abnormally low levels of several bacterial species compared to healthy controls, including Faecalibacterium prausnitzii (F. prausnitzii) and Eubacterium rectale. These health-promoting bacteria produce a short chain fatty acid called butyrate, a bacterial metabolite, or by-product, that plays an important role in maintaining gut health. An acetate-producing bacterium was also reduced in samples obtained from people with ME/CFS.

More detailed metabolomic analyses confirmed that a reduction in these bacteria was associated with reduced butyrate production in ME/CFS. Butyrate is the primary energy source for cells that line the gut, providing up to 70% of their energy requirements, support for the gut immune system, and protection against diseases of the digestive tract. Butyrate, tryptophan, and other metabolites detected in the blood are important for regulating immune, metabolic, and endocrine functions.

While species of butyrate-producing bacteria decreased, there were increased levels of nine other species in ME/CFS, including Enterocloster bolteae and Ruminococcus gnavus, which are associated with autoimmune diseases and inflammatory bowel disease, respectively.

Dr. Williams’ group also reported that an abundance of F. prausnitzii was inversely associated with fatigue severity in ME/CFS, suggesting a possible link between gut bacteria and disease symptoms. More research is needed to determine if differences in the gut microbiome are a consequence or cause of symptoms.

The findings indicate that imbalances in these 12 species of bacteria could be used as biomarkers for ME/CFS classification, potentially providing consistent, measurable targets to improve diagnosis.

The gut microbiome is an ecosystem with complex interactions between bacteria, where microbes can exchange or compete for nutrients, metabolites, or other molecular signals. Researchers found notable differences in the network of species interactions in people with ME/CFS—including unique interactions between F. prausnitzii and other species. This indicates that there is an extensive rewiring of bacterial networks in ME/CFS.

“In addition to differences in individual species in ME/CFS, focusing a lens on community interaction dynamics may add greater specificity to the broad definition of dysbiosis, distinguishing between other diseases in which the gut microbiome becomes imbalanced,” said Dr. Williams. “This is also important for generating new testable hypotheses about the underlying mechanisms and mediators of dysbiosis in ME/CFS and may eventually inform strategies to correct these imbalances.”

A balanced microbiome is also essential for a variety of neural systems, especially immune regulation and coupling between energy metabolism and blood supply in the brain, as well as the function of the nerves that supply the gut.

In another study at the Jackson Laboratory in Farmington, Connecticut, Julia Oh, Ph.D.(link is external), associate professor, and Derya Unutmaz, M.D., professor, teamed up with other ME/CFS experts to study microbiome abnormalities in different phases of ME/CFS. Dr. Oh’s team collected and analyzed clinical data, fecal samples, and blood samples from 149 people with ME/CFS who had been diagnosed within the previous four years (74 short-term) or who had been diagnosed more than 10 years ago (75 long-term) and 79 healthy controls.

The results showed that the short-term group had less microbial diversity, while the long-term group established a stable, but individualized gut microbiome similar to healthy controls. Dr. Oh and her colleagues found lower levels of several butyrate-producing species, including F. prausnitzii, especially in the short-term participants. There was also a reduction in species associated with tryptophan metabolism in all ME/CFS participants compared to controls.

Dr. Oh’s group also collected detailed clinical and lifestyle data from participants. By combining these data with genetic and metabolome data, the team developed a way to accurately classify and differentiate ME/CFS from healthy controls. Using this approach, they found that individuals with long-term ME/CFS had a more balanced microbiome but showed more severe clinical symptoms and progressive metabolic irregularities compared to the other groups.

Both studies identify potential biomarkers for ME/CFS, which may inform diagnostic tests and disease classification. Understanding the connection between disturbances in the gut microbiome and ME/CFS may also guide the development of new therapeutics.

Additional research is required to learn more about the pathophysiological implications of butyrate and other metabolite deficiencies in ME/CFS. Future studies will determine how gut microbe disturbances contribute to symptoms, including changes during disease progression.

The studies were funded in part by the NIH’s ME/CFS Collaborative Research Network(link is external), a consortium supported by multiple institutes and centers at NIH, consisting of three collaborative research centers and a data management coordinating center. The research network was established in 2017 to help advance research on ME/CFS. The research was supported by NINDS grant U54NS105539, National Institute of Allergy and Infectious Diseases grants U54AI138370 and R56AI120724, and anonymous donors through the Crowdfunding Microbe Discovery Project.

Long Covid and Neurodegenerative Disease

Abstract:

Brain fog with compromised ability to concentrate has been the most frequent Long Covid (LC) complaint. This is due to an increased TGF beta/IFN gamma with consequently increased bradykinin (BKN), especially in Caucasian females. Brain and lung blood vessels “leak.” This same ratio is increased in Alzheimer’s disease (AD), but decreased in Parkinson’s disease (PD), because CD4+ and CD8+ T cells are differentially affected by the invading associated viruses, e.g., SARS CoV2, HIV, ….

In Covid-19 CD147 receptors on immune cells are critical in generating the increased TGF beta/IFN gamma and those on endothelial cells, platelets, and erythrocytes are critical to the abnormal microvascular blood flow. ACE2 receptors on pneumocytes and enterocytes enable pulmonary and GI entry, initiating gut dysbiosis.

Epigenetics, methylation, magnesium, vitamin D, the B vitamins, and antioxidants suggest that these issues can be surmounted. Biochemical, physiologic, and epidemiologic data are analyzed to answer these questions. An LC model is presented and discussed in the context of the most recent research. Suggestions to avoid these and other worrisome concerns are included. Other topics discussed include estrogen, the gut microbiome, type 2 diabetes (T2D), and homocysteine.

Source: Chambers, P. Long Covid and Neurodegenerative Disease. Preprints 2023, 2023020027 (doi: 10.20944/preprints202302.0027.v1) https://www.preprints.org/manuscript/202302.0027/v1 (Full text available as PDF file)

 

Clinical Characteristics in the Acute Phase of COVID-19 That Predict Long COVID: Tachycardia, Myalgias, Severity, and Use of Antibiotics as Main Risk Factors, While Education and Blood Group B Are Protective

Abstract:

Background: Risk factors for developing long COVID are not clearly established. The present study was designed to determine if any sign, symptom, or treatment of the acute phase, or personal characteristics of the patient, is associated with the development of long COVID.
Methods: A cohort study was carried out, randomly selecting symptomatic COVID-19 patients and not vaccinated. The severity of the acute illness was assessed through the number of compatible COVID-19 symptoms, hospitalizations, and the symptom severity score using a 10-point visual analog scale.
Results: After multivariate analysis, a severity score ≥8 (RR 2.0, 95%CI 1.1–3.5, p = 0.022), hospitalization (RR 2.1, 95%CI 1.0–4.4, p = 0.039), myalgia (RR 1.9, 95%CI 1.08–3.6, p = 0.027), tachycardia (RR 10.4, 95%CI 2.2–47.7, p = 0.003), and use of antibiotics (RR 2.0, 95%CI 1.1–3.5, p = 0.022), was positively associated with the risk of having long COVID. Higher levels of education (RR 0.6, 95%CI 0.4–0.9, p = 0.029) and type positive B blood group (B + AB, RR 0.44, 95%CI 0.2–0.9, p = 0.044) were protective factors. The most important population attributable fractions (PAFs) for long COVID were myalgia (37%), severity score ≥8 (31%), and use of antibiotics (27%).
Conclusions: Further studies in diverse populations over time are needed to expand the knowledge that could lead us to prevent and/or treat long COVID.
Source: Guzman-Esquivel J, Mendoza-Hernandez MA, Guzman-Solorzano HP, Sarmiento-Hernandez KA, Rodriguez-Sanchez IP, Martinez-Fierro ML, Paz-Michel BA, Murillo-Zamora E, Rojas-Larios F, Lugo-Trampe A, Plata-Florenzano JE, Delgado-Machuca M, Delgado-Enciso I. Clinical Characteristics in the Acute Phase of COVID-19 That Predict Long COVID: Tachycardia, Myalgias, Severity, and Use of Antibiotics as Main Risk Factors, While Education and Blood Group B Are Protective. Healthcare. 2023; 11(2):197. https://doi.org/10.3390/healthcare11020197 https://www.mdpi.com/2227-9032/11/2/197 (Full text)

Toxin-like Peptides from the Bacterial Cultures Derived from Gut Microbiome Infected by SARS-CoV-2—New Data for a Possible Role in the Long COVID Pattern

Abstract:

It has been 3 years since the beginning of the SARS-CoV-2 outbreak, however it is as yet little known how to care for the acute COVID-19 and long COVID patients. COVID-19 clinical manifestations are of both pulmonary and extra-pulmonary types. Extra-pulmonary ones include extreme tiredness (fatigue), shortness of breath, muscle aches, hyposmia, dysgeusia, and other neurological manifestations.
In other autoimmune diseases, such as Parkinson’s disease (PD) or Alzheimer’s Disease (AD), it is well known that role of acetylcholine is crucial in olfactory dysfunction. We have already observed the presence of toxin-like peptides in plasma, urine, and faecal samples from COVID-19 patients, which are very similar to molecules known to alter acetylcholine signaling.  After observing the production of these peptides in bacterial cultures, we have performed additional proteomics analyses to better understand their behavior and reported the extended data from our latest in vitro experiment.
It seems that the gut microbiome continues to produce toxin-like peptides also after the decrease of RNA SARS-CoV-2 viral load at molecular tests. These toxicological interactions between the gut/human microbiome bacteria and the virus suggest a new scenario in the study of the clinical symptoms in long COVID and also in acute COVID-19 patients. It is discussed that in the bacteriophage similar behavior, the presence of toxins produced by bacteria continuously after viral aggression can be blocked using an appropriate combination of certain drugs.
Source: Brogna C, Cristoni S, Brogna B, Bisaccia DR, Marino G, Viduto V, Montano L, Piscopo M. Toxin-like Peptides from the Bacterial Cultures Derived from Gut Microbiome Infected by SARS-CoV-2—New Data for a Possible Role in the Long COVID Pattern. Biomedicines. 2023; 11(1):87. https://doi.org/10.3390/biomedicines11010087 https://www.mdpi.com/2227-9059/11/1/87 (Full text)

Mild SARS-CoV-2 infection results in long-lasting microbiota instability

Abstract:

Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.

IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.

Source: Vaibhav Upadhyay, Rahul Suryawanshi, Preston Tasoff, Maria McCavitt-Malvido, G. Renuka Kumar, Victoria Wong Murray, Cecilia Noecker, Jordan E. Bisanz, Yulin Hswen, Connie Ha, Bharat Sreekumar, Irene P. Chen, Susan V Lynch, Melanie Ott, Sulggi Lee, Peter J. Turnbaugh. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv 2022.12.07.519508; doi: https://doi.org/10.1101/2022.12.07.519508  https://www.biorxiv.org/content/10.1101/2022.12.07.519508v1.full (Full text)

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome

Abstract:

Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months.

Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.

Source: Liu Q, Su Q, Zhang F, Tun HM, Mak JWY, Lui GC, Ng SSS, Ching JYL, Li A, Lu W, Liu C, Cheung CP, Hui DSC, Chan PKS, Chan FKL, Ng SC. Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome. Nat Commun. 2022 Nov 10;13(1):6806. doi: 10.1038/s41467-022-34535-8. PMID: 36357381; PMCID: PMC9648868. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9648868/ (Full text)

The role of gut microbiota in etiopathogenesis of long COVID syndrome

To the editor.

COVID-19, a novel infectious disease caused by SARS-CoV-2 first emerged on November 17, 2019 had a high fatality rate and affected millions of people around the world [1]. The involvement of lung gut axis and the identification of viral RNA in feces of infected patients has drawn attention to a possible fecal-oral transmission route of SARS-CoV-2 [2].

Recent research shows a potential connection between long-term COVID-19 and dysbiosis of the gut flora. Long COVID-19 infection or post-acute COVID-19 syndrome is seen after weeks or months after the initial COVID-19 infection is characterized by complications and lingering symptoms such as fatigue, muscle weakness, and sleeplessness. Up to 3 out of 4 individuals report at least one symptom six months after recovering from COVID-19 infection, making it a relatively prevalent condition [3]. Long COVID may develop as a result of a heightened immune response, cell damage, or physiological effects of COVID-19 infection.

The gut microbiome, the billions of bacteria, fungus, and other microbes that live in the digestive tract, has been linked to COVID-19 severity and may possibly have an impact on the healing process, according to a growing body of research [4]. Researchers at the Chinese University of Hong Kong’s Center for Gut Microbiota Research discovered a clue in 2020.

When compared to healthy controls, persons with COVID-19 had unique changes in their gut microbiota, or the population of bacteria that live in their gut [5]. Early reports from Wuhan suggested that 2–10% of COVID-19 patients experienced gastrointestinal (GI) symptoms, such as diarrhoea, however a recent meta-analysis found that up to 20% of patients with COVID-19 had GI symptoms. SARS-CoV-2 virus was found in anal swabs and stool samples in over half of COVID-19 patients, suggesting that the digestive tract could be an extrapulmonary location for virus multiplication and activity [6, 7].

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Source: Kaushik P, Kumari M, Singh NK, Suri A. The role of gut microbiota in etiopathogenesis of long COVID syndrome. Horm Mol Biol Clin Investig. 2022 Nov 1. doi: 10.1515/hmbci-2022-0079. Epub ahead of print. PMID: 36317311. https://www.degruyter.com/document/doi/10.1515/hmbci-2022-0079/html (Full text)

Current knowledge about Chronic fatigue syndrome / myalgic encephalomyelitis (CFS/ME) causes – summary

Abstract:

Chronic Fatigue Syndrome (CFE) is a severe and disabling disease whose etiology has not yet been elucidated. This implies the lack of a specific biomarker for the diagnosis of PE, and no causal treatment.

There are a number of diagnostic criteria that facilitate the diagnosis of PE, but it is still a diagnosis with exclusion. This chapter reviews the scientific literature systematically, summarizing the available knowledge about the probable etiology of Chronic Fatigue Syndrome.

The current topic of the influence of SARS-Cov-2 virus infection on the development of symptoms of IPC was also taken into account in particular.

A clear explanation of the etiology of PE is necessary for the further development of scientific knowledge about the Chronic Fatigue Syndrome.

Source: PRYLIŃSKA-JAŚKOWIAK, Monika & KOŻUCHOWSKI, Marcin. Current knowledge about Chronic fatigue syndrome / myalgic encephalomyelitis (CFS/ME) causes – summary. Journal of Education, Health and Sport [online]. 13 September 2022, T. 12, nr 9, s. 712–719. [accessed 26.9.2022]. DOI 10.12775/JEHS.2022.12.09.084.  https://apcz.umk.pl/JEHS/article/view/39954 https://apcz.umk.pl/JEHS/article/view/39954/33214 (Full text)

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with an unclear etiology and pathogenesis. Both an involvement of the immune system and gut microbiota dysbiosis have been implicated in its pathophysiology. However, potential interactions between adaptive immune responses and the microbiota in ME/CFS have been incompletely characterized. Here, we profiled antibody responses of patients with severe ME/CFS and healthy controls against microbiota and viral antigens represented as a phage-displayed 244,000 variant library.

Patients with severe ME/CFS exhibited distinct serum antibody epitope repertoires against flagellins of Lachnospiraceae bacteria. Training machine learning algorithms on this antibody-binding data demonstrated that immune responses against gut microbiota represent a unique layer of information beyond standard blood tests, providing improved molecular diagnostics for ME/CFS.

Together, our results point toward an involvement of the microbiota-immune axis in ME/CFS and lay the foundation for comparative studies with inflammatory bowel diseases and illnesses characterized by long-term fatigue symptoms, including post-COVID-19 syndrome.

Source: Vogl T, Kalka IN, Klompus S, Leviatan S, Weinberger A, Segal E. Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients. Sci Adv. 2022 Sep 23;8(38):eabq2422. doi: 10.1126/sciadv.abq2422. Epub 2022 Sep 23. PMID: 36149952. https://www.science.org/doi/10.1126/sciadv.abq2422 (Full text)

The COVID-19 Pandemic and Post-Infection Irritable Bowel Syndrome: What Lies Ahead for Gastroenterologists

Clinical Problem

An increasingly recognized subset of patients develops post-infection sequelae also described as long COVID or postacute COVID-19 syndrome (PACS). These patients experience a myriad of neurologic, respiratory, cardiac, psychiatric, and/or GI symptoms that persist for 4 weeks or more from the initial diagnosis of SARS-CoV-2.

Epidemiology

In a survey study of 749 survivors, 29% reported at least 1 new chronic GI symptom 6 months after their COVID-19 infection, with heartburn, constipation, diarrhea, and abdominal pain being the most common.2 Of the patients with abdominal pain, 39% met Rome IV criteria for irritable bowel syndrome (IBS). Other studies also reported a 30%–40% prevalence of GI PACS. Additionally, COVID-19 infection was associated with worsening severity of preexisting IBS symptoms. Some risk factors for GI PACS include the presence of GI symptoms during acute infection, psychiatric diagnoses (depression, anxiety) both pre- and post-COVID-19, need for hospitalization during acute illness, and loss of smell and taste. Infectious gastroenteritis is an established risk-factor for development of disorders of gut-brain interaction (DGBI), particularly post-infection IBS (PI-IBS). Many of the risk factors for GI PACS described are also known predisposing factors for PI-IBS, with some exceptions, such as female gender, a risk factor for PI-IBS but not consistently associated with GI PACS. In addition to IBS, other de novo DGBIs, such as functional dyspepsia, heartburn, chest pain, and dysphagia, can be experienced in the spectrum of GI PACS.

Disease Mechanisms

The pathophysiology of PACS including that of the GI manifestations is incompletely understood; however, it is likely multifactorial (Figure 1). Epithelial invasion by SARS-CoV-2 is substantiated by the high expression levels of angiotensin-converting enzyme-2 on the enterocytes and colonocytes. The angiotensin-converting enzyme-2 is a negative regulator of the renin-angiotensin system and has a protective cellular role, including in the intestinal tract. Following the entry of SARS-CoV-2 in the cell, angiotensin-converting enzyme-2 protein is downregulated, resulting in an increase in angiotensin-II, the likely molecular mechanism of severe acute respiratory syndrome and systemic inflammatory response development with this coronavirus. Intestinal microbial dysbiosis has also been associated with acute SARS-CoV-2 infection and PACS. Long-term respiratory dysfunction after COVID-19 is associated with altered gut microbiota and persistently elevated lipopolysaccharide-binding protein levels. One study showed that dysbiosis in COVID-19 patients continued throughout their hospitalizations and up to 21 days from disease onset, with a decrease in health-promoting, short-chain fatty acid–forming bacteria.3 Gut microbiome of patients with PACS was characterized by higher levels of Ruminococcus gnavus and Bacteroides vulgatus, and lower levels of Faecalibacterium prausnitzii. Interestingly, presence of butyrate-producing bacteria showed an inverse correlation with development of PACS at 6 months.4 A recent study also suggested that salivary microbiome during acute infection may predict the development of GI PACS.5

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Source: Walter W. Chan and Madhusudan Grover. The COVID-19 Pandemic and Post-Infection Irritable Bowel Syndrome: What Lies Ahead for Gastroenterologists. Published: August 06, 2022. DOI: https://doi.org/10.1016/j.cgh.2022.05.044 (Full text)