Days before a national lockdown in the U.S., Daniel McDonald realized his life’s work had put a unique tool in his hands to fight COVID-19. The assay kits his team was about to have made by the tens of thousands could be repurposed to help understand the novel coronavirus that causes the disease. McDonald is Read article >

The post Gut Instinct: Human Microbiome May Reveal COVID-19 Mysteries appeared first on The Official NVIDIA Blog.

Modifying bacteria found in the guts of bees could help protect the insects against lethal infections affecting hives worldwide

Title: Kids' 'Microbiome' May Play Key Role in Asthma
Category: Health News
Created: 12/24/2019 12:00:00 AM
Last Editorial Review: 12/24/2019 12:00:00 AM

Title: 'Microbiome' May Be Key to Autism Symptoms
Category: Health News
Created: 5/1/2019 12:00:00 AM
Last Editorial Review: 5/2/2019 12:00:00 AM

ABSTRACT

Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.

IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

ABSTRACT

Microbes affect vertebrates on timescales from daily to evolutionary, and the cumulative effect of these interactions is immense. However, how microbiomes compare across (host) species is poorly understood, as most studies focus on relatively few species. A recent mBio article by S. J. Song, J. G. Sanders, F. Delsuc, J. Metcalf, et al. (mBio 11:e02901-19, 2019, https://doi.org/10.1128/mBio.02901-19) expands our collective understanding of the vertebrate microbiome by analyzing ~900 species. They demonstrate that patterns within mammals contrast with those within birds. Their results suggest many hypotheses about the role of host ecology and evolution on microbiome variation. Bats, the only volant mammals, appear to contradict many of the general mammal microbiome trends, in some ways resembling birds. What role has powered flight, and the evolution thereof, played in microbiome structure and function? Comparative methods, mechanistic hypotheses, and theory will elucidate this exciting question (and others) that we can ask using Song, Sanders et al.’s data and results.

ABSTRACT

Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests that commensal species within the UT and urogenital tract (UGT) microbiomes, such as Lactobacillus crispatus, may act to protect against colonization with uropathogens. However, the mechanisms and fundamental biology of the urinary microbiome-host relationship are not understood. The ability to measure and characterize the urinary microbiome has been enabled through the development of next-generation sequencing and bioinformatic platforms that allow for the unbiased detection of resident microbial DNA. Translating technological advances into clinical insight will require further study of the microbial and genomic ecology of the urinary microbiome in both health and disease. Future diagnostic, prognostic, and therapeutic options for the management of UTI may soon incorporate efforts to measure, restore, and/or preserve the native, healthy ecology of the urinary microbiomes.

Clostridioides difficileDiagnosticsMetabolomicsMicrobiome

Antibiotics revolutionized the treatment of infectious diseases; however, it is now clear that broad-spectrum antibiotics alter the composition and function of the host’s microbiome. The microbiome plays a key role in human health, and its perturbation is increasingly recognized as contributing to many human diseases. Widespread broad-spectrum antibiotic use has also resulted in the emergence of multidrug-resistant pathogens, spurring the development of pathogen-specific strategies such as monoclonal antibodies (MAbs) to combat bacterial infection. Not only are pathogen-specific approaches not expected to induce resistance in nontargeted bacteria, but they are hypothesized to have minimal impact on the gut microbiome. Here, we compare the effects of antibiotics, pathogen-specific MAbs, and their controls (saline or control IgG [c-IgG]) on the gut microbiome of 7-week-old, female, C57BL/6 mice. The magnitude of change in taxonomic abundance, bacterial diversity, and bacterial metabolites, including short-chain fatty acids (SCFA) and bile acids in the fecal pellets from mice treated with pathogen-specific MAbs, was no different from that with animals treated with saline or an IgG control. Conversely, dramatic changes were observed in the relative abundance, as well as alpha and beta diversity, of the fecal microbiome and bacterial metabolites in the feces of all antibiotic-treated mice. Taken together, these results indicate that pathogen-specific MAbs do not alter the fecal microbiome like broad-spectrum antibiotics and may represent a safer, more-targeted approach to antibacterial therapy.

The pks⁺ E. coli metabolite colibactin caused a unique mutational signature in intestinal organoids.

A large international study found that the composition of the intestinal microbiome can predict clinical outcomes in patients undergoing allogenic hematopoietic-cell transplant (HCT) for blood cancers. The findings may help assess patients' transplantation-related mortality risk and aid in developing interventions to prevent or mitigate microbiome changes that affect HCT outcomes.

While smoking is inextricably linked to oral/head and neck cancer (HNSCC), only a small fraction of smokers develop HNSCC. Thus, we have sought to identify other factors, which may influence the development of HNSCC in smokers including microbiology. To determine microbial associations with HNSCC among tobacco users, we characterized oral microbiome composition in smokers with and without HNSCC. 16S rRNA MiSeq sequencing was used to examine the oral mucosa microbiome of 27 smokers with (cases) and 24 without HNSCC (controls). In addition, we correlated previously reported levels of DNA damage with the microbiome data. Smokers with HNSCC showed lower microbiome richness compared with controls (q = 0.012). Beta-diversity analyses, assessed as UniFrac (weighted and unweighted) and Bray–Curtis distances, showed significant differences in oral mucosal microbiome signatures between cases and controls (r² = 0.03; P = 0.03) and higher interindividual microbiome heterogeneity in the former (q ≤ 0.01). Higher relative abundance of Stenotrophomonas and Comamonadaceae and predicted bacterial pathways mainly involved in xenobiotic and amine degradation were found in cases compared with controls. The latter, in contrast, exhibited higher abundance of common oral commensals and predicted sugar degradation pathways. Finally, levels of DNA damage in the oral cavity were correlated with the microbiome profiles above. Oral microbiome traits differ in smokers with and without HNSCC, potentially informing the risk of eventual HNSCC and shedding light into possible microbially mediated mechanisms of disease. These findings present data that may be useful in screening efforts for HNSCC among smokers who are unable to quit.

RBX2660 may bring an innovative therapeutic option to patients suffering from C. diff

uBiome, a San Francisco startup that sells commercial tests that use DNA sequencing to identify what microbes are in a person's stool or, for one test, in the vagina, has raised $83 million from venture capitalists to fund an entrée into drug development.

Swiss drugmaker Ferring and its Rebiotix subsidiary have announced a world first with a microbiome-based…

Unfortunately it's not an improvement.

The diet appears to act on gut bacteria in a way that helps hinder physical frailty and reduce cognitive decline in older age, researchers find.

The secret to a diet that makes the microbes in your gut healthy, for fighting obesity and disease

Highlights: On behalf of ISPEN 2019, Medindia interviewed Dr. BS Ramakrishna to throw light on the evolving ro

Nutrition and diet have a profound impact on microbial composition in the gut, according to a study. The findings of the study are published in the journal iNutrition Reviews/i.

Vaping alters the mouth's microbiome and makes e-cigarette users more prone to inflammation and infection, stated new study led by researchers at NYU College of Dentistry.

Netherton syndrome, a rare skin disease caused by a single genetic mutation, is exacerbated by the presence of two common Staphylococcal bacteria living

There is now strong evidence that microbiomes play an important role in human health, as there are clear linkages to many major non-communicable diseases. This report assesses the key policy challenges for innovation in the microbiome. It argues that if such a promising scientific field is to lead to innovative applications, policies on science and innovation must be improved in five areas.

TALK OF THE TOWN: Chloe Delevingne is nurturing her 'gut microbiome' by guzzling an uber-trendy probiotic drink called Symprove which contains four strains of live bacteria.

Online Resource

Sharing microbes around the house; roundup of daily news.

Seth Bordenstein discusses how our genes affect the composition of our microbiome, influencing our health, and David Grimm talks with Sarah Crespi about the origins of the Basque language, the benefits of being raised in a barn, and how some flying ants lost their wings. Hosted by Susanne Bard. [Image credit: Decaseconds/CC BY-NC 2.0, via flickr

Sarah Crespi talks to Sam Smits about how our microbial passengers differ from one culture to the next—are we losing diversity and the ability to fight chronic disease? For our books segment, Jen Golbeck talks with Vyvyan Evans about his book The Emoji Code: The Linguistics Behind Smiley Faces and Scaredy Cats. Listen to previous podcasts. [Image: Woodlouse/Flickr; Music: Jeffrey Cook]

Orla Smith, editor of Science Translational Medicine joins host Sarah Crespi to talk about what has changed in the past 10 years of microbiome research, what’s getting close to being useful in treatment, and how strong, exactly, the research is behind those probiotic yogurts. When you’re sick, sleeping is restorative—it helps your body recover from nasty infections. Meagan Cantwell speaks with Amita Sehgal, professor of neuroscience at the University of Pennsylvania and an investigator at Howard Hughes Medical Institute in Chevy Chase, Maryland, about the process of discovering a gene in fruit flies that links sleep and immune function. This week’s episode was edited by Podigy. Download the transcript (PDF) Listen to previous podcasts. About the Science Podcast [Music: Jeffrey Cook]

Micro-organisms live inside everything from the human gut to coral—but where do they come from? Host Meagan Cantwell talks to Staff Writer Elizabeth Pennisi about the first comprehensive survey of microbes in Hawaii’s Waimea Valley, which revealed that plants and animals get their unique microbiomes from organisms below them in the food chain or the wider environment. Going global, Meagan then speaks with Erle Ellis, professor of geography and environmental science at the University of Maryland, Baltimore County, about a project that aggregated the expertise of more than 250 archaeologists to map human land use over the past 10,000 years. This detailed map will help fine-tune climate models. This week’s episode was edited by Podigy. Ads on this show: Science Sessions Podcast; Kroger Download a transcript (PDF)  Listen to previous podcasts. About the Science Podcast [Image: Chris Couderc/Flickr; Music: Jeffrey Cook]

As we age, our skin changes, and so too do the bugs that live there

This podcast discusses the latest research into the workings of the lung microbiome and how it will affect future diagnosis and treatment of respiratory diseases. Related article: The Lung Microbiome: Key to Respiratory Ills?

Interview with Julia A. Segre, Ph.D., author of Manipulating the Human Microbiome to Manage Disease

Hayden Library - QR41.2.C6713 2018

Toys inspire biology, biology inspires toys

An inhibitor of starch-digesting enzymes stunts the growth of certain gut bacteria

An inhibitor of starch-digesting enzymes stunts the growth of certain gut bacteria