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Best SIBO Diet: 9 Foods We Need To Eat And Avoid

Small intestinal bacterial overgrowth, or SIBO, is just like it sounds: your small intestine has a lot of bacteria in it. Check out our recommended SIBO diet food list below to find out what you need to eat versus avoid. RELATED: The 9 Best Foods To Eat When You’re Constipated, According to a Microbiome Scientist In this article: Recommended Diets for SIBO Foods to Eat in Your SIBO Diet Foods to Avoid in Your SIBO Diet Customizing Your SIBO Diet: 9 Foods to Eat and Avoid What is SIBO? SIBO is a digestive disorder that occurs when the small intestine has excessive bacteria. While it is essential to have bacteria in the gut to aid in digestion, too much of it can cause some complications. What is a SIBO Diet? This diet involves the elimination of bacteria-induced inflammation in the digestive tract, particularly in the small intestine. Carbs that are difficult to digest or...
Gut balances keep you from losing weight

3 Ways Gut Imbalances Keep You from Losing Weight — and 7 Ways to...

We know… another thing that depends on our gut?! Yep, it’s true — a healthy, balanced gut acts as the solid foundation for successful weight loss. When your gut is imbalanced, you’ll have a hard time losing weight. Here are three reasons why.

How Do Interactions Between Gut Bacteria and Fungi Exacerbate Crohn’s Disease?

Case Western Reserve School of Medicine and University Hospitals Cleveland Medical Center researcher receives NIH funding to investigate Scientists have known that bacteria in the gut, along with environmental and genetic factors, contribute to the debilitating intestinal ailment of Crohn’s disease (CD). But in 2016, Mahmoud A Ghannoum, professor and director of the Center for Medical Mycology at Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, was the first to identify a specific fungus in humans that interacted with bacteria in the development of the disease. Now, to learn precisely how that fungus interacts with bacteria to trigger CD, Ghannoum has received a five-year, $3 million grant from the National Institutes of Health. His investigation will involve innovative molecular and cellular technologies, to delete specific genes in the fungus and note the effects on the inflammation that is a marker for CD using powerful microscopic analysis. “Uncovering how the...
Effects of a Novel Probiotic Combination on Pathogenic Bacterial-Fungal Polymicrobial Biofilms

Effects of a Novel Probiotic Combination on Pathogenic Bacterial-Fungal Polymicrobial Biofilms

Abstract: Dysbiosis of the gut microbiome has been implicated in inflammatory bowel diseases. We have shown that levels of Candida tropicalis, along with those of Escherichia coli and Serratia marcescens, are significantly elevated in Crohn’s disease (CD) patients. Here, we evaluated the ability of a novel probiotic to prevent and treat polymicrobial biofilms (PMB) formed by C. tropicalis with E. coli and S. marcescens. Since Candida albicans has been reported to be elevated in CD patients, we investigated the interactions of C. albicans with these bacterial species in biofilm formation. We determined whether the interaction between Candida spp. and bacteria is specific by using Trichosporon inkin and Saccharomyces fibuligera as comparators. Additionally, the effects of probiotics on C. albicans germination and biofilm formation were determined. To determine the ability of the probiotic to prevent or treat mature biofilms, probiotic filtrate was added to the PMB at early (prevention) and mature (treatment) phases. Biofilm thickness and architecture were assessed by confocal scanning laser microscopy....
2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century”

2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of...

Abstract: The National Institutes of Health (NIH) organized a three-day human microbiome research workshop, August 16–18, 2017, to highlight the accomplishments of the 10-year Human Microbiome Project program, the outcomes of the investments made by the 21 NIH institutes and Centers which now fund this area, and the technical challenges and knowledge gaps which will need to be addressed in order for this field to advance over the next 10 years. This report summarizes the key points in the talks, round table discussions, and Joint Agency Panel from this workshop. Download Full Paper:
The Gut Microbiome as a Major Regulator of the Gut-Skin Axis

The Gut Microbiome as a Major Regulator of the Gut-Skin Axis

Abstract: The adult intestine hosts a myriad of diverse bacterial species that reside mostly in the lower gut maintaining a symbiosis with the human habitat. In the current review, we describe the neoteric advancement in our comprehension of how the gut microbiota communicates with the skin as one of the main regulators in the gut-skin axis. We attempted to explore how this potential link affects skin differentiation and keratinization, its influence on modulating the cutaneous immune response in various diseases, and finally how to take advantage of this communication in the control of different skin conditions. Download Full Paper:
Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with...

Abstract: The effect of smoking on microbial dysbiosis and the potential consequence of such shift on markers of HIV disease is unknown. Here we assessed the relationship of microbial dysbiosis with smoking and markers of HIV disease. Download Full Paper:
The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease– Like Ileitis

The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–...

Abstract: Background: Epidemiological studies indicate that the use of artificial sweeteners doubles the risk for Crohn’s disease (CD). Herein, we experimentally quantified the impact of 6-week supplementation with a commercial sweetener (Splenda; ingredients sucralose maltodextrin, 1:99, w/w) on both the severity of CD-like ileitis and the intestinal microbiome alterations using SAMP1/YitFc (SAMP) mice. Methods: Metagenomic shotgun DNA sequencing was first used to characterize the microbiome of ileitis-prone SAMP mice. Then, 16S rRNA microbiome sequencing, quantitative polymerase chain reaction, fluorescent in situ hybridization (FISH), bacterial culture, stereomicroscopy, histology, and myeloperoxidase (MPO) activity analyses were then implemented to compare the microbiome and ileitis phenotype in SAMP with that of control ileitis-free AKR/J mice after Splenda supplementation. Results: Metagenomics indicated that SAMP mice have a gut microbial phenotype rich in Bacteroidetes, and experiments showed that Helicobacteraceae did not have an exacerbating effect on ileitis. Splenda did not increase the severity of stereomicroscopic/histological) ileitis; however, biochemically, ileal MPO activity was increased in SAMP...
The Mycobiome in HIV

The Mycobiome in HIV

Abstract: Purpose of Review—There are a limited number of studies investigating the association between the microbiome and HIV. Although the majority of these published investigations have focused on the role of the bacterial community (bacteriome) in this setting, a handful of studies have also characterized the role of the mycobiome in HIV-infected individuals. This review will summarize the most recent reports pertaining to the role of the fungal community in HIV. Recent findings—Differences in the composition of the oral and respiratory mycobiome in HIV-infected individuals compared to uninfected individuals have been reported. Summary—Our review shows that studies investigating the role of the mycobiome in the setting of HIV are severely lacking. With recent advances in our understanding of the composition of the human microbiome, investigations into the role of the bacteria and fungus comprising the overall microbiota and how the two interact to influence each other and the host is crucial. Download Full...
Bacteriome and mycobiome associations in oral tongue cancer

Bacteriome and mycobiome associations in oral tongue cancer

Abstract: Squamous cell carcinoma of the oral (mobile) tongue (OMTC), a non-human papilloma virus-associated oral cancer, is rapidly increasing without clear etiology. Poor oral hygiene has been associated with oral cancers, suggesting that oral bacteriome (bacterial community) and mycobiome (fungal community) could play a role. While the bacteriome is increasingly recognized as an active participant in health, the role of the mycobiome has not been studied in OMTC. Tissue DNA was extracted from 39 paired tumor and adjacent normal tissues from patients with OMTC. Microbiome profiling, principal coordinate, and dissimilarity index analyses showed bacterial diversity and richness, and fungal richness, were significantly reduced in tumor tissue (TT) compared to their matched non-tumor tissues (NTT, P<0.006). Firmicutes was the most abundant bacterial phylum, which was significantly increased in TT compared to NTT (48% vs. 40%, respectively; P=0.004). Abundance of Bacteroidetes and Fusobacteria were significantly decreased in TT compared to matched NTT...
The Mycobiome: Impact on Health and Disease States

The Mycobiome: Impact on Health and Disease States

Introduction: Research efforts by mycologists over the past few years finally established the fungal community and its previously overlooked members as crucial components of the microbiome. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. Ongoing research is describing the fungal community and is providing new insights into biological mechanisms by which multidirectional interactions between the microbiome, their genomes (metagenome), metabolites (metabolome), and the human host ultimately affect health and/or disease states. Download Full Paper:
The mycobiome: Role in health and disease, and as a potentialprobiotic target in gastrointestinal disease

The mycobiome: Role in health and disease, and as a potentialprobiotic target in gastrointestinal...

Abstract: human gastrointestinal (GI) tract is home to trillions of microorganisms, some beneficial and otherspotentially harmful. Recent advances in science have allowed us to identify the multitude of organismsinhabiting the GI tract and parse out those that play a role in inflammatory bowel disease (IBD). Unfortu-nately, most research has focused on studying only the bacteria while ,overlooking a key player, fungus.In order to address this issue, we have focused our efforts on studying the fungal community in the GItract known as the mycobiome. We found that patients with Crohn’s disease (CD) tend to have muchhigher levels of the fungus Candida tropicalis compared to their healthy family members, as well as twobacteria, Escherichia coli and Serratia marcescens. Furthermore, we showed that these three organismsworked together to form robust biofilms capable of exacerbating intestinal inflammation. Herein, wediscuss the role of the mycobiome in health and disease, and highlight the importance of maintainingbalance...
Cooperative Evolutionary Strategy between the Bacteriome and Mycobiome

Cooperative Evolutionary Strategy between the Bacteriome and Mycobiome

Abstract: Nonhealing chronic wounds are all unique in origin and circumstance, and attempting to isolate a single etiology for the failure of a wound to heal is daunting. Wounds represent complex systems of multispecies fungal and bacterial biofilms. The survival strategies of interactive microbial communities have led to cooperative evolutionary strategies that culminate in biofilm formation. In microbial dysbiosis, biofilms are beneficial to both bacterial and fungal communities but detrimental to the host. Fungi benefit by a surge in their virulence factors, while bacteria become tolerant to antibacterials as a consequence of living under the protective umbrella of the biofilm matrix. This interkingdom cooperation negatively impacts the host, as the fungi and bacteria produce extracellular enzymes that inflict tissue damage, leading to an increase in proinflammatory cytokines, which results in oxidative damage and apoptotic cell death. Download Full Paper:
Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease

Abstract: Crohn’s disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their nondiseased first-degree relatives (NCDR) in 9 familial clusters living in northern France-Belgium and in healthy individuals from 4 families living in the same area (non-CD unrelated ). Principal component, diversity, and abundance analyses were conducted, and CD-associated inter- and intrakingdom microbial correlations were determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms. CD and NCDR groups clustered together in the mycobiome but not in the bacteriome. Microbiotas of familial (CD and NCDR) samples were distinct from those of nonfamilial (NCDU) samples. The abundance of Serratia marcescens and Escherichia coli was elevated in CD patients, while that of beneficial bacteria was decreased. The abundance of the fungus Candida tropicalis was significantly higher...

The Mycobiome

The largely overlooked resident fungal community plays a critical role in human health and disease. At a workshop held at the National Institutes of Health (NIH) last September on the role of human microbiota in infectious disease, I was disheartened not to hear a single talk on the fungal community—the mycobiome. Disheartened, but not surprised. Ignoring the fungal kingdom is nothing new. More than five years ago, my colleague and I tried to draw attention to this issue in a letter published in Microbe, recommending that the Human Microbiome Project should investigate not just people’s bacterial inhabitants, but the fungal and viral commensal communities as well. While research on the human virome has increased in recent years, the scientific community has not heeded our advice with regard to the fungal components of the microbiome. As of November 2015, only 269 of more than 6,000 Web of Science search results for...
Mycobiota in gastrointestinal diseases

Mycobiota in gastrointestinal diseases

Abstract: New insights gained through the use of state-of-the-art technologies, including next-generation sequencing, are starting to reveal that the association between the gastrointestinal tract and the resident mycobiota (fungal community) is complex and multifaceted, in which fungi are active participants influencing health and disease. Characterizing the human mycobiome (the fungi and their genome) in healthy individuals showed that the gastrointestinal tract contains 66 fungal genera and 184 fungal species, with Candida as the dominant fungal genera. Although fungi have been associated with a number of gastrointestinal diseases, characterization of the mycobiome has mainly been focused in patients with IBD and graft-versus-host disease. In this Review, we summarize the findings from studies investigating the relationship between the gut mycobiota and gastrointestinal diseases, which indicate that fungi contribute to the aggravation of the inflammatory response, leading to increased disease severity. A model explaining the mechanisms underlying the role of the mycobiota in gastrointestinal diseases is also presented. Our understanding of the contribution of the...
Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi

Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic...

Abstract: Oral microbiota contribute to health and disease, and their disruption may influence the course of oral diseases. Here, we used pyrosequencing to characterize the oral bacteriome and mycobiome of 12 HIV-infected patients and matched 12 uninfected controls. The number of bacterial and fungal genera in individuals ranged between 8–14 and 1–9, among uninfected and HIV-infected participants, respectively. The core oral bacteriome (COB) comprised 14 genera, of which 13 were common between the two groups. In contrast, the core oral mycobiome (COM) differed between HIV-infected and uninfected individuals, with Candida being the predominant fungus in both groups. Among Candida species, C. albicans was the most common (58% in uninfected and 83% in HIV-infected participants). Furthermore, 15 and 12 bacteria-fungi pairs were correlated significantly within uninfected and HIV-infected groups, respectively. Increase in Candida colonization was associated with a concomitant decrease in the abundance of Pichia, suggesting antagonism. We found that Pichia...
Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

Abstract: The oral microbiome–organisms residing in the oral cavity and their collective genome–are critical components of health and disease. The fungal component of the oral microbiota has not been characterized. In this study, we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity of 20 healthy individuals, using the panfungal internal transcribed spacer (ITS) primers. Our results revealed the ‘‘basal’’ oral mycobiome profile of the enrolled individuals, and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. Among these genera, 39 were present in only one person, 16 genera were present in two participants, and 5 genera were present in three people, while 15 genera (including non-culturable organisms) were present in $4 (20%) participants. Candida species were the most frequent (isolated from 75% of participants), followed by Cladosporium (65%), Aureobasidium, Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). Four of...