For over 300 years, scientists have primarily studied bacteria using liquid cultures or flat 2D plates in laboratory settings

Ferguson, D K; Li, C; Jiang, C; Chakraborty, A; Grasby, S E; Hubert, C R J. Science of the Total Environment vol. 722, 137258, 2020 p. 1-12, https://doi.org/10.1016/j.scitotenv.2020.137258
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We naturally pick up microorganisms as we move about the world. Now, researchers have developed an AI tool that accurately links you to a particular location using a sample of the bugs you’ve collected on your travels – like a bacterial satellite navigation system.

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Category: AI in Health, Medical Innovations, Body & Mind

Tags: Microbiome, Bacteria, Location, Satellite Navigation, Lund University

I’m concerned about bacterial growth in my emergency shower/eyewash equipment. What proactive steps can I take to keep my equipment clean and free of bacteria?

To figure out what dietary ingredients promote helpful bacteria, several studies have looked at the effects of individual fibers and probiotics.

In recent times, there has been a greater focus on hygiene in the workplace, likely spurred on by the COVID pandemic. While some germs are completely harmless, others can cause unpleasant illnesses. The chances of a germ surviving largely depends on the type of species, the surface where it is present, and other factors such as ambient temperature or solar radiation.

The title compound, 3-[(benzo-1,3-dioxol-5-yl)amino]-4-meth­oxy­cyclo­but-3-ene-1,2-dione, C12H9NO5 (3), is a precursor to an anti­mycobacterial squaramide. Block-shaped crystals of a monoclinic form (3-I, space group P21/c, Z = 8, Z' = 2) and needle-shaped crystals of a triclinic form (3-II, space group P-1, Z = 4, Z' = 2) were found to crystallize concomitantly. In both crystal forms, R22(10) dimers assemble through N—H⋯O=C hydrogen bonds. These dimers are formed from crystallographically unique mol­ecules in 3-I, but exhibit crystallographic Ci symmetry in 3-II. Twinning by pseudomerohedry was encountered in the crystals of 3-II. The conformations of 3 in the solid forms 3-I and 3-II are different from one another but are similar for the unique mol­ecules in each polymorph. Density functional theory (DFT) calculations on the free mol­ecule of 3 indicate that a nearly planar conformation is preferred.

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development.

OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied pico­second–millisecond spectroscopic intermediates.

The title compound, C15H15F3N2O3S, crystallizes in the monoclinic system, space group I2/a, with Z = 8. As expected, the nine-membered heterobicyclic system is virtually planar and the cyclo­hexyl group adopts a chair conformation. There is structural evidence for intra­molecular N—S⋯O chalcogen bonding between the benziso­thia­zolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N—S bond [N—S⋯O = 162.7 (1)°]. In the crystal, the mol­ecules form centrosymmetric dimers through C—H⋯O weak hydrogen bonding between a C—H group of the electron-deficient benzene ring and the benzo­thia­zolinone carbonyl O atom with an R22(10) motif. In contrast to the previously described N-acyl 7-nitro-5-(tri­fluoro­meth­yl)benzo[d]iso­thia­zol-3(2H)-ones, the title N-cyclo­hexyl­methyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro.

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The molecular mechanism used by many bacteria to kill neighboring cells has redundancy built into its genetic makeup, which could allow for the mechanism to be expressed in different environments, say researchers at Penn State and the University of Wisconsin-Madison. Their new study provides insights into the molecular mechanisms of competition among bacteria. "Many organisms, including humans, acquire bacteria from their environment," said Tim Miyashiro, a biochemist and molecular biologist at Penn State and the leader of the research team. "These bacteria can contribute to functions within the host organism, like how our gut bacteria help us digest food. We're interested in the interactions among bacteria cells, and between bacteria and their hosts, to better understand these mutually beneficial symbiotic relationships." Cells of the bioluminescent bacteria Vibrio fisheri take up residence in the light organ of newly hatched bobtail squid. At night, the bacteria produce a blue glow that researchers believe obscures a squid's silhouette and helps protect it from predators. The light organ has pockets, or crypts, in the squid's skin that provide nutrients and a safe environment for the bacteria. "When the squid hatches, it doesn't yet have any bacteria in its light organ," said Miyashiro. "But bacteria in the environment quickly colonize the squid's light organ." Some of these different bacteria strains can coexist, but others can't. "Microbial symbioses are essentially universal in animals, and are crucial to the health and development of both partners," says Irwin Forseth, a program director in the National Science Foundation's Division of Integrative Organismal Systems, which funded the research. "The results from this study highlight the role small genetic changes can play in microbe interactions. Increased understanding will allow us to better predict organisms' performance in changing environments."

Image credit: Andrew Cecere

Scientists have built a new sensor that can detect the potentially deadly E.coli bacteria in 15-20 minutes, much faster than traditional lab tests. E.coli can be transmitted in contaminated food and water, posing particular risks to children and the elderly. In the late spring of 2011 a serious outbreak of E.coli bacteria sickened thousands of people in Germany and killed more than 50.

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In a new study, Siva Umapathy and Deepak Kumar Saini’s teams have demonstrated another application for this combination: Quickly identifying bacterial pathogens in different types of clinical samples.

Certain antibiotic resistance genes are easily transferred from one bacterial species to another, and can move between farm animals and the human gut. A team led by Chinese researchers has characterized this "mobile resistome," which they say is largely to blame for the spread of antibiotic resistance. They found that many antibiotic resistance genes that are shared between the human and animal gut microbiome are also present in multiple human pathogens. These findings are published September 9 in Applied and Environmental Microbiology, a journal of the American Society for Microbiology.

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Many bacteria possess molecular spear guns, which they fire at enemies and rivals, thus putting them out of action. The tips of these nano-spear guns, known as Type VI secretion system (T6SS), are loaded with toxic molecules that lead to death of their adversaries. However, sometimes close related bacteria come under fire.

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n-tech projects that smart antibacterial and antiviral products will reach US$1.3 billion by 2025 driven by efforts to combat Covid-19 and provide safer workplace, health care and improved public health

COVID-19 has propelled the market for antimicrobials of all types over the past year, this n-tech study takes a look at business potential for smart materials with antimicrobial functionality in a post vaccine world.

Scientists are starting to learn about what composes a healthy microbiome, such as the bacterial species and the molecules they generate...

Two new research studies have demonstrated that bacteria are able to retain and pass down 'memories' of temporary, short changes ...

Scientists are starting to learn about what composes a healthy microbiome, such as the bacterial species and the molecules they generate...

Two new research studies have demonstrated that bacteria are able to retain and pass down 'memories' of temporary, short changes ...

Scientists are starting to learn about what composes a healthy microbiome, such as the bacterial species and the molecules they generate...

Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen  Nature.com

In response to an explosion of “toxic mold” claims in 2000-2001, the insurance industry acted in unprecedented unison to universally get rid of all claims related in any way to mold. They didn’t stop at just excluding claims from mold; they threw bacteria into the exclusion as well.

Technique may revolutionize the design of scaffolds for regenerative medicine applications.

The findings open the door for new microbial-based therapy for anxiety and depression, according to UCC.

Read more: Gut bacteria affects stress response, UCC scientists find

El madridista se rompió el cruzado el 6 de septiembre de 2022 ante el Celtic y ahí empezó su calvario Leer

In recent times, there has been a greater focus on hygiene in the workplace, likely spurred on by the COVID pandemic. While some germs are completely harmless, others can cause unpleasant illnesses.

GSA is testing the water systems at 1,400 federal facilities to create a baseline and remediate any findings of Legionella and other problems.

The post Legionella bacteria in your office’s water? Don’t be alarmed first appeared on Federal News Network.

Location: Electronic Resource- 

Gut microbiome disruption in male mice increases disease risk in offspring, indicating that preconception paternal health status can affect the next generation.

Following recent hurricanes, reports of "flesh-eating" bacteria in Florida have emerged, but these bacteria, which exist year-round, don't actually consume flesh.

It may not feel like it when the worst stomach flu of your life has you in its grip, but often, the best thing to do when you have E. coli is to rest and keep drinking beverages with electrolytes.

I recently switched over to using a vinegar-based spray cleaner (just vinegar, water, and rubbing alcohol), to clean my kitchen. It works wonderfully for me, and I love that by using it I'm saving money and reducing my exposure to harsh chemicals. — Read the rest

The post The science of vinegar: what happens to bacteria under a microscope appeared first on Boing Boing.

Boris Macek
Feb 1, 2008; 7:299-307
Research

Jason M. Ridlon
Feb 1, 2006; 47:241-259
Reviews

Recent studies have suggested that innate immune responses exhibit characteristics associated with memory linked to modulations in both vertebrates and invertebrates. However, the diverse evolutionary paths taken, particularly within the invertebrate taxa, should lead to similarly diverse innate immunity memory processes. Our understanding of innate immune memory in invertebrates primarily comes from studies of the fruit fly Drosophila melanogaster, the generality of which is unclear. Caenorhabditis elegans typically inhabits soil harboring a variety of fatal microbial pathogens; for this invertebrate, the innate immune system and aversive behavior are the major defensive strategies against microbial infection. However, their characteristics of immunological memory remains infantile. Here we discovered an immunological memory that promoted avoidance and suppressed innate immunity during reinfection with bacteria, which we revealed to be specific to the previously exposed pathogens. During this trade-off switch of avoidance and innate immunity, the chemosensory neurons AWB and ADF modulated production of serotonin and dopamine, which in turn decreased expression of the innate immunity-associated genes and led to enhanced avoidance via the downstream insulin-like pathway. Therefore, our current study profiles the immune memories during C. elegans reinfected by pathogenic bacteria and further reveals that the chemosensory neurons, the neurotransmitter(s), and their associated molecular signaling pathways are responsible for a trade-off switch between the two immunological memories.

Animals can sense the presence of microbes in their tissues and mobilize their own defenses by recognizing and responding to conserved microbial structures (often called microbe-associated molecular patterns (MAMPs)). Successful host defenses may kill the invaders, yet the host animal may fail to restore homeostasis if the stimulatory microbial structures are not silenced. Although mice have many mechanisms for limiting their responses to lipopolysaccharide (LPS), a major Gram-negative bacterial MAMP, a highly conserved host lipase is required to extinguish LPS sensing in tissues and restore homeostasis. We review recent progress in understanding how this enzyme, acyloxyacyl hydrolase (AOAH), transforms LPS from stimulus to inhibitor, reduces tissue injury and death from infection, prevents prolonged post-infection immunosuppression, and keeps stimulatory LPS from entering the bloodstream. We also discuss how AOAH may increase sensitivity to pulmonary allergens. Better appreciation of how host enzymes modify LPS and other MAMPs may help prevent tissue injury and hasten recovery from infection.

Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable “free” iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.

Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division, the machinery responsible for PG synthesis localizes mid-cell, at the septum, under the control of a multiprotein complex called the divisome. In Escherichia coli, septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. Interestingly, a short sequence of FtsN (Leu75–Gln93, known as EFtsN) was shown to be essential and sufficient for its functioning in vivo, but what exactly this sequence is doing remained unknown. Here, we show that EFtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its biosynthetic glycosyltransferase (GTase) activity. We also report the crystal structure of PBP1b in complex with EFtsN, which demonstrates that EFtsN binds at the junction between the GTase and UB2H domains of PBP1b. Interestingly, mutations to two residues (R141A/R397A) within the EFtsN-binding pocket reduced the activation of PBP1b by FtsN but not by the lipoprotein LpoB. This mutant was unable to rescue the ΔponB-ponAts strain, which lacks PBP1b and has a thermosensitive PBP1a, at nonpermissive temperature and induced a mild cell-chaining phenotype and cell lysis. Altogether, the results show that EFtsN interacts with PBP1b and that this interaction plays a role in the activation of its GTase activity by FtsN, which may contribute to the overall septal PG synthesis and regulation during cell division.

Michael E. Abrams
Dec 1, 2020; 61:1538-1538
Images in Lipid Research

Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.

In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11–13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24–32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nt from the 3´ end and 9 nt from the 5´ end flanking the damage. To test this model, we used the in vivo excision assay and the excision repair sequencing genome-wide repair mapping method developed in our laboratory to determine the repair pattern and genome-wide repair map of Mycobacterium smegmatis. We find that M. smegmatis, which possesses homologs of the Escherichia coli uvrA, uvrB, and uvrC genes, removes cyclobutane pyrimidine dimers from the genome in a manner identical to the prokaryotic pattern by incising 7 nt 5´ and 3 or 4 nt 3´ to the photoproduct, and performs transcription-coupled repair in a manner similar to E. coli.

While no candy is truly healthy, some options are better for your gut than others. And there are ways you can help wake your gut from its sugar "spell" after holiday indulgence.

Shiaoching Gong
Sep 12, 2007; 27:9817-9823
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