Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.

The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both and in the dextran sodium sulfate (DSS) mouse model of colitis.

Ion Spectroscopy in the Context of the Diffuse Interstellar Bands: A Case Study with the Phenylacetylene Cation.

Identification of the molecular carriers of diffuse interstellar bands (DIBs) requires gas phase electronic spectra of suitable candidate structures. Recording the spectra of these in the laboratory is challenging because they include large, carbon-rich molecules, many of which are likely to be ionic. The electronic spectra of ions are often obtained using action spectroscopy methods, which can induce small perturbations to the absorption characteristics and hinder comparison with astronomical observations.

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.

Unlabelled: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic.

Worming into infancy: Exploring helminth-microbiome interactions in early life.

There is rapidly growing awareness of microbiome assembly and function in early-life gut health. Although many factors, such as antibiotic use and highly processed diets, impinge on this process, most research has focused on people residing in high-income countries. However, much of the world's population lives in low- and middle-income countries (LMICs), where, in addition to erratic antibiotic use and suboptimal diets, these groups experience unique challenges.

Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting.

The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria.

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting.

The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use a functional assay to identify and isolate gut bacteria from healthy human volunteers that take up different glycans.

Characterizing the Effect of Amylase Inhibitors on Maltodextrin Metabolism by Gut Bacteria Using Fluorescent Glycan Labeling.

Diet-derived polysaccharides are an important carbon source for gut bacteria and shape the human gut microbiome. Acarbose, a compound used clinically to treat type 2 diabetes, is known to inhibit the growth of some bacteria on starches based on its activity as an inhibitor of α-glucosidases and α-amylases. In contrast to acarbose, montbretin A, a new drug candidate for the treatment of type 2 diabetes, has been reported to be more specific for the inhibition of α-amylase, notably human pancreatic α-amylase.

Correction: Sutcliffe et al. Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut. 2021, , 455.

In the original publication [...

Using shrimp shells and concrete to mitigate leaching for metals from waste rock.

The capability of shrimp shells or construction demolition concrete as amendments to immobilize elements, primarily Pb and Zn, generated from mine waste weathering, was investigated via standard batch leaching test (L/S 10 cm/g, 24 h). The effect of the amendment was tested at waste rock-to-residue ratios 9:1, 9.5:0.

Dog ownership and mental health among community-dwelling older adults: A systematic review.

Background: The population is ageing, and psychiatric disorders are common in older people. Those are associated with worsened quality of life. Although the positive relationship between dog ownership and physical health has been documented, data on mental health are scarcer, especially in community-dwelling older adults.

OnePetri: Accelerating Common Bacteriophage Petri Dish Assays with Computer Vision.

Bacteriophage plaque enumeration is a critical step in a wide array of protocols. The current gold standard for plaque enumeration on Petri dishes is through manual counting. However, this approach is not only time-consuming and prone to human error but also limited to Petri dishes with countable number of plaques resulting in low throughput.

The Mini Colon Model: a benchtop multi-bioreactor system to investigate the gut microbiome.

fermentation systems allow for the investigation of gut microbial communities with precise control of various physiological parameters while decoupling confounding factors from the human host. Current systems, such as the SHIME and Robogut, are large in footprint, lack multiplexing, and have low experimental throughput. Alternatives which address these shortcomings, such as the Mini Bioreactor Array system, are often reliant on expensive specialized equipment, which hinders wide replication across labs.

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis.

Background: Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut.

Boosted Spontaneous Formation of High-Aspect Ratio Nanopeaks on Ultrafast Laser-Irradiated Ni Surface.

The capacity to synthesize and design highly intricated nanoscale objects of different sizes, surfaces, and shapes dramatically conditions the development of multifunctional nanomaterials. Ultrafast laser technology holds great promise as a contactless process able to rationally and rapidly manufacture complex nanostructures bringing innovative surface functions. The most critical challenge in controlling the growth of laser-induced structures below the light diffraction limit is the absence of external order associated to the inherent local interaction due to the self-organizing nature of the phenomenon.

Early-Life Exposure to Environmental Contaminants Perturbs the Sperm Epigenome and Induces Negative Pregnancy Outcomes for Three Generations via the Paternal Lineage.

Due to the grasshopper effect, the Arctic food chain in Canada is contaminated with persistent organic pollutants (POPs) of industrial origin, including polychlorinated biphenyls and organochlorine pesticides. Exposure to POPs may be a contributor to the greater incidence of poor fetal growth, placental abnormalities, stillbirths, congenital defects and shortened lifespan in the Inuit population compared to non-Aboriginal Canadians. Although maternal exposure to POPs is well established to harm pregnancy outcomes, paternal transmission of the effects of POPs is a possibility that has not been well investigated.

Changes in Gut Bacterial Translation Occur before Symptom Onset and Dysbiosis in Dextran Sodium Sulfate-Induced Murine Colitis.

Longitudinal studies on the gut microbiome that follow the effect of a perturbation are critical in understanding the microbiome's response and succession to disease. Here, we use a dextran sodium sulfate (DSS) mouse model of colitis as a tractable perturbation to study how gut bacteria change their physiology over the course of a perturbation. Using single-cell methods such as flow cytometry, bioorthogonal noncanonical amino acid tagging (BONCAT), and population-based cell sorting combined with 16S rRNA sequencing, we determine the diversity of physiologically distinct fractions of the gut microbiota and how they respond to a controlled perturbation.

The human gut microbiome and health inequities.

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities.

A phingerprint for rheumatoid arthritis development?

The human gut virome has become increasingly associated with health and disease. In this issue of Cell Host & Microbe, Mangalea et al. (2021) find differences in viromes of individuals at risk for rheumatoid arthritis (RA), suggesting that phages may play a role in RA and provide a path for biomarker development.

A one-generation reproductive toxicity study of the mycotoxin ochratoxin A in Fischer rats.

Ochratoxin A (OTA) is a mycotoxin produced by Aspergillus and Penicillium molds. Grain-based foods account for most human dietary exposures to OTA. OTA is a teratogen, but its reproductive and developmental effects are poorly understood.

Co-disposal of lignite fly ash and coal mine waste rock for neutralisation of AMD.

Waste rocks (WRs) from a lignite-producing coalfield and fly ash (FA) produced from the same lignite have been investigated in this study with a primary objective to determine the potential for co-disposal of WRs and FA to reduce the environmental contamination. Mixing WRs with FA and covering WRs with FA have been investigated. Particle size effect caused ≤2 mm particles to produce low pH (~2) and metal-laden leachates, indicating higher sulphide minerals' reactivity compared to larger particles (≤10 mm, pH ~ 4).

Self-Organization Regimes Induced by Ultrafast Laser on Surfaces in the Tens of Nanometer Scales.

A laser-irradiated surface is the paradigm of a self-organizing system, as coherent, aligned, chaotic, and complex patterns emerge at the microscale and even the nanoscale. A spectacular manifestation of dissipative structures consists of different types of randomly and periodically distributed nanostructures that arise from a homogeneous metal surface. The noninstantaneous response of the material reorganizes local surface topography down to tens of nanometers scale modifying long-range surface morphology on the impact scale.

Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut.

Many bacteria carry bacteriophages (bacterial viruses) integrated in their genomes in the form of prophages, which replicate passively alongside their bacterial host. Environmental conditions can lead to prophage induction; the switching from prophage replication to lytic replication, that results in new bacteriophage progeny and the lysis of the bacterial host. Despite their abundance in the gut, little is known about what could be inducing these prophages.

Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota.

Changes in bacterial diversity in the human gut have been associated with many conditions, despite not always reflecting changes in bacterial activity. Methods linking bacterial identity to function are needed for improved understanding of how bacterial communities adapt and respond to their environment, including the gut. Here, we optimized bioorthogonal non-canonical amino acid tagging (BONCAT) for the gut microbiota and combined it with fluorescently activated cell sorting and sequencing (FACS-Seq) to identify the translationally active members of the community.