Research Roundup: 20 New and Interesting Articles on the Human Microbiome

Medical background with 3D virus cells and DNA strandI’ve read many scientific articles lately. Some were good and interesting, others were not. In today’s blog post I’ve collected the ones that I found most intriguing, so that you get to read them too. All of the papers are about the human microbiome, which is the main topic of today’s research roundup. Some of the articles I link to are original research papers, whereas others are articles that explain the key findings of a study.

If you have any comments to the articles I share in today’s post, feel free to share them in the comment section below the post.

Okay, let’s get to it…

1. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice

Abstract: The early life microbiome plays important roles in host immunological and metabolic development. Because the incidence of type 1 diabetes (T1D) has been increasing substantially in recent decades, we hypothesized that early-life antibiotic use alters gut microbiota, which predisposes to disease. Using non-obese diabetic mice that are genetically susceptible to T1D, we examined the effects of exposure to either continuous low-dose antibiotics or pulsed therapeutic antibiotics (PAT) early in life, mimicking childhood exposures. We found that in mice receiving PAT, T1D incidence was significantly higher, and microbial community composition and structure differed compared with controls. In pre-diabetic male PAT mice, the intestinal lamina propria had lower Th17 and Treg proportions and intestinal SAA expression than in controls, suggesting key roles in transducing the altered microbiota signals. PAT affected microbial lipid metabolism and host cholesterol biosynthetic gene expression. These findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating T1D onset in non-obese diabetic mice. Read more…

2. Healing effect of fecal microbiota transplantation lasts for a long time

The researchers in the University of Helsinki and Helsinki University Hospital have studied in detail the intestinal microbiota of 14 patients treated with a faecal microbiota transplant. The patients suffered from recurrent Clostridium difficile -infection, also known as antibiotic associated diarrhea, and they had not responded to antibiotic treatment. After the faecal microbiota transplantation therapy, the patient’s microbiota was followed for a year.

The researchers found out that the patient’s intestinal microbiota highly resembled the donor’s microbiota and this composition remained stable through-out the 1-year follow-up period. Read more…

3. Captivity humanizes the primate microbiome.

Significance: Trillions of bacteria live in the primate gut, contributing to metabolism, immune system development, and pathogen resistance. Perturbations to these bacteria are associated with metabolic and autoimmune human diseases that are prevalent in Westernized societies. Herein, we measured gut microbial communities and diet in multiple primate species living in the wild, in a sanctuary, and in full captivity. We found that captivity and loss of dietary fiber in nonhuman primates are associated with loss of native gut microbiota and convergence toward the modern human microbiome, suggesting that parallel processes may be driving recent loss of core microbial biodiversity in humans. Read more…

4. Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome.

… Using this intestinal microbiota signature, we found IBS symptom severity to be negatively associated with microbial richness, exhaled CH4, presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species. This microbiota signature could not be explained by differences in diet or use of medications. Read more…

5. The Microbiome: a Revolution in Treatment for Rheumatic Diseases?

A growing number of microbiota constituents such as Prevotella copri, Porphyromonas gingivalis, and Collinsella have been correlated or causally related to rheumatic disease. The microbiome has a marked effect on the immune system. Our understanding of immune pathways modulated by the microbiota such as the induction of T helper 17 (Th17) cells and secretory immunoglobulin A (IgA) responses to segmented filamentous bacteria continues to expand. In addition to the gut microbiome, bacterial communities of other sites such as the mouth, lung, and skin have also been associated with the pathogenesis of rheumatic diseases. Strategies to alter the microbiome or to alter the immune activation from the microbiome might play a role in the future therapy for rheumatic diseases. Read more…

6. Delivering beneficial bacteria to the GI tract

Jaklenec and colleagues developed a way to coat bacteria with polymer layers that protect them from the acids and bile salts found in the digestive tract. When the microbes reach the intestine, they attach to the intestinal lining and begin reproducing.

“The bacteria are delivered and they adhere to the intestinal wall, where they survive much better than noncoated bacteria,” says Koch Institute postdoc Aaron Anselmo, the paper’s first author. Read more…

7. Fecal bacteria linked to body fat

A new link between the diversity of bacteria in human poo — known as the human fecal microbiome — and levels of abdominal body fat, has been identified by scientists. The research provides further evidence of possible genetic influences on obesity, through heritable bacteria found in the fecal microbiome. Read more…

8. Food-poisoning bacteria may be behind Crohn’s disease

Using a mouse model of Crohn’s disease, the researchers discovered that acute infectious gastroenteritis caused by common food-poisoning bacteria accelerates the growth of adherent-invasive E. coli (AIEC) — a bacterium that has been linked to the development of Crohn’s.

Even after the mice had eliminated the food-poisoning bacteria, researchers still observed increased levels of AIEC in the gut, which led to worsened symptoms over a long period of time. Read more…

9. Intestinal Dysbiosis and Yeast Isolation in Stool of Subjects with Autism Spectrum Disorders.

High frequency of gastrointestinal yeast presence in ASD subjects was shown through a simple cultural approach (Candida spp. in 57.5 % of ASDs and no controls); the identification of aggressive form (pseudo-hyphae presenting) of Candida spp. at light microscope means that adhesion to intestinal mucosa is facilitated. Dysbiosis appears sustained by lowered Lactobacillus spp. and decreased number of Clostridium spp. Absence of C. difficilis and its toxins in both ASDs and controls is also shown. Low-mild gut inflammation and augmented intestinal permeability were demonstrated together with the presence of GI symptoms. Significant linear correlation was found between disease severity (CARs score) and calprotectin and Clostridium spp. presence. Also GI symptoms, such as constipation and alternating bowel, did correlate (multivariate analyses) with the increased permeability to lactulose. The present data provide rationale basis to a possible specific therapeutic intervention in restoring gut homeostasis in ASDs. Read more…

10. Newborn gut microbiome predicts later allergy and asthma, study finds
Microbial byproducts link particular early-life gut microbes to immune dysfunction

The microbes living in a baby’s gut during its first month of life may directly impact the developing immune system, leading to a higher risk of allergies and asthma later in childhood, according to a new study. The findings highlight the importance of developing early interventions to improve microbial health in young infants. Read more…

11. ICU patients lose helpful gut bacteria within days of hospital admission

The microbiome of patients admitted to the intensive care unit (ICU) at a hospital differs dramatically from that of healthy patients, according to a new study. Researchers analyzing microbial taxa in ICU patients’ guts, mouth and skin reported finding dysbiosis, or a bacterial imbalance, that worsened during a patient’s stay in the hospital. Compared to healthy people, ICU patients had depleted populations of commensal, health-promoting microbes and higher counts of bacterial taxa with pathogenic strains. Read more…

12. Associations of Bowel Movement Frequency with Risk of Cardiovascular Disease and Mortality among US Women.

… After adjustment for dietary intake, lifestyle, medication use, and other risk factors, as compared with women with daily bowel movement, having bowel movements more than once daily was significantly associated with increased risk of CVD (hazard ratio [HR]: 1.13; 95% confidence interval [CI]: 1.05-1.21), total mortality (HR: 1.17; 95% CI: 1.12-1.22), and cardiovascular mortality (HR: 1.17; 95% CI: 1.07-1.28). With further adjustment for body mass index and diabetes status, the association with total mortality remained significant (HR: 1.10; 95% CI: 1.06-1.15), whereas the associations with incident CVD and cardiovascular mortality were no longer significant. Our results suggest increased bowel movement frequency is a potential risk factor for premature mortality. Read more…

13. Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view

Our findings lend support to the notion that the enteric ecosystem co-evolved in the ancient selective environments of our presiding forager legacy, thus complementing human physiology in present day hunter-gatherers. In addition to the abundance of hexoses (simple sugars), that seems to be indicative of a diet rich in microbiota-accessible carbohydrates (MAC)3, the high presence of sphingolipids and glycerophospholipids, together with low levels of amino acids, suggests a robustly healthy gut metabolic profile that is specifically poor in factors known to trigger or contribute to the typical inflammation-based Western diseases. Read more…

14. Fungus in humans identified for first time as key factor in Crohn’s disease

The researchers found strong fungal-bacterial interactions in those with Crohn’s disease: two bacteria (Escherichia coli and Serratia marcescens) and one fungus (Candida tropicalis) moved in lock step. The presence of all three in the sick family members was significantly higher compared to their healthy relatives, suggesting that the bacteria and fungus interact in the intestines. Additionally, test-tube research by the Ghannoum-led team found that the three work together (with the E. coli cells fusing to the fungal cells and S. marcescens forming a bridge connecting the microbes) to produce a biofilm — a thin, slimy layer of microorganisms found in the body that adheres to, among other sites, a portion of the intestines — which can prompt inflammation that results in the symptoms of Crohn’s disease. Read more…

15. Associations between Periodontal Microbiota and Death Rates.

In conclusion, our analysis suggested that specific combinations of periodontal bacteria, even without inducing clinically significant periodontitis, may have a significant impact on human cause-specific death rates. More mechanistic and human observational studies are needed before a clinical trial could be implemented to confirm our findings. If an etiological relationship of specific periodontal microbiota to death rates is established, increased mortality could be transmittable via the transfer of oral microbiota. In that case, developing personalized strategies and maintaining a healthy oral microbiota, beyond that against periodontitis, would be important to manage the increased mortality risk. Read more…

16. Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder.

Conclusion: Our results provide direct evidence, for the first time, that individuals with lower Bifidobacterium and/or Lactobacillus counts are more common in patients with MDD compared to controls. Our findings provide new insight into the pathophysiology of MDD and will enhance future research on the use of pro- and prebiotics in the treatment of MDD. Read more…

17. Lactic acid bacteria differentially regulate filamentation in two heritable cell types of the human fungal pathogen Candida albicans.

Microorganisms rarely exist as single species in natural environments. The opportunistic fungal pathogen Candida albicans and lactic acid bacteria (LAB) are common members of the microbiota of several human niches such as the mouth, gut and vagina. Lactic acid bacteria are known to suppress filamentation, a key virulence feature of C. albicans, through the production of lactic acid and other metabolites. Here we report that C. albicans cells switch between two heritable cell types, white and opaque, to undergo filamentation to adapt to diversified environments. We show that acidic pH conditions caused by LAB and low temperatures support opaque cell filamentation, while neutral pH conditions and high temperatures promote white cell filamentation. The cAMP signalling pathway and the Rfg1 transcription factor play major roles in regulating the responses to these conditions. This cell type-specific response of C. albicans to different environmental conditions reflects its elaborate regulatory control of phenotypic plasticity. Read more…

18. Beneficial bacteria may protect breasts from cancer

Bacteria that have the potential to abet breast cancer are present in the breasts of cancer patients, while beneficial bacteria are more abundant in healthy breasts, where they may actually be protecting women from cancer, according a study. These findings may lead ultimately to the use of probiotics to protect women against breast cancer. Read more…

19. A single species of gut bacteria can reverse autism-related social behavior in mice

The absence of a one specific species of gut bacteria causes social deficits in mice, researchers report. By adding this bacteria species back to the guts of affected mice, the researchers were able to reverse some of their behavioral deficits, which are reminiscent of symptoms of autism spectrum disorders (ASDs) in humans. The investigators are now looking to explore the effects of probiotics on neurodevelopmental disorders in future work. Read more…

20. Microbiota as a mediator of cancer progression and therapy.

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. Read more…

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Comments

  1. Interesting articles, Eirik. Thanks for your efforts.

  2. Ditto to the above. I often share your articles as I just did now!

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