Marcos Pires

A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes.

Gramibactin is a bacterial siderophore with a diazeniumdiolate ligand system

Gramibactin is a bacterial siderophore with a diazeniumdiolate ligand system, Published online: 30 July 2018; doi:10.1038/s41589-018-0101-9

Plant-associated rhizosphere bacteria produce gramibactin, a cyclic lipodepsipeptide siderophore that tightly binds iron via an unexpected functional group, the N-nitrosohydroxylamine (diazeniumdiolate) moieties of the amino acid graminine.

Designed peptides that assemble into cross-α amyloid-like structures

Designed peptides that assemble into cross-α amyloid-like structures, Published online: 30 July 2018; doi:10.1038/s41589-018-0105-5

Structural analysis reveals how certain designed peptides adopt unusual spiraling cross-α amyloid-like structures and also rearrange to helical polymers upon mutation of small nonpolar residues that are critical for packing and stabilization.

Jacobson et al. show that the composition of the host microbiota controls intestinal expansion of the enteric pathogen S. Typhimurium. They demonstrate that Bacteroides spp. mediate colonization resistance to S. Typhimurium infection through production of the short-chain fatty acid propionate, which directly limits pathogen growth by disrupting intracellular pH homeostasis.

The development of a genetically encoded toolkit of surface-bound nanobodies and antigens in E. coli allows for precise manipulation of cell-cell adhesion and rational design of diverse self-assembled multicellular patterns and morphologies.

ABSTRACT

The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems ("EcoFABs") along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

ABSTRACT

Macrophages are critical to innate immunity due to their ability to phagocytose bacteria. The macrophage phagolysosome is a highly acidic organelle with potent antimicrobial properties, yet remarkably, ingested Staphylococcus aureus replicates within this niche. Herein we demonstrate that S. aureus requires the GraXRS regulatory system for growth within this niche, while the SaeRS and AgrAC two-component regulatory systems and the α-phenol soluble modulins are dispensable. Importantly, we find that it is exposure to acidic pH that is required for optimal growth of S. aureus inside fully acidified macrophage phagolysosomes. Exposure of S. aureus to acidic pH evokes GraS signaling, which in turn elicits an adaptive response that endows the bacteria with increased resistance to antimicrobial effectors, such as antimicrobial peptides, encountered inside macrophage phagolysosomes. Notably, pH-dependent induction of antimicrobial peptide resistance in S. aureus requires the GraS sensor kinase. GraS and MprF, a member of the GraS regulon, play an important role for bacterial survival in the acute stages of systemic infection, where in murine models of infection, S. aureus resides within liver-resident Kupffer cells. We conclude that GraXRS represents a vital regulatory system that functions to allow S. aureus to evade killing, prior to commencement of replication, within host antibacterial immune cells.

IMPORTANCE S. aureus can infect any site of the body, including the microbicidal phagolysosome of the macrophage. The ability of S. aureus to infect diverse niches necessitates that the bacteria be highly adaptable. Here we show that S. aureus responds to phagolysosome acidification to evoke changes in gene expression that enable the bacteria to resist phagolysosomal killing and to promote replication. Toxin production is dispensable for this response; however, the bacteria require the sensor kinase GraS, which transduces signals in response to acidic pH. GraS is necessary for phagolysosomal replication and survival of S. aureus in the acute stage of systemic infection. Disruption of this S. aureus adaptation would render S. aureus susceptible to phagocyte restriction.

Human skin commensals augment Staphylococcus aureus pathogenesis

Human skin commensals augment <i>Staphylococcus aureus</i> pathogenesis, Published online: 16 July 2018; doi:10.1038/s41564-018-0198-3

Skin commensals increase host susceptibility to Staphylococcus aureus infection through a liver macrophage and peptidoglycan-dependent axis.

by Ruben Dario Arroyo-Olarte, Laura Thurow, Vera Kozjak-Pavlovic, Nishith Gupta

The birth and subsequent evolution of optogenetics has resulted in an unprecedented advancement in our understanding of the brain. Its outstanding success does usher wider applications; however, the tool remains still largely relegated to neuroscience. Here, we introduce selected aspects of optogenetics with potential applications in infection biology that will not only answer long-standing questions about intracellular pathogens (parasites, bacteria, viruses) but also broaden the dimension of current research in entwined models. In this essay, we illustrate how a judicious integration of optogenetics with routine methods can illuminate the host–pathogen interactions in a way that has not been feasible otherwise.

Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude

Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude, Published online: 11 July 2018; doi:10.1038/s41467-018-05079-7

Unwanted uptake in the liver and limited accumulation in target organs is a major obstacle to targeted drug delivery. Here, the authors report on the hitchhiking of nanocarriers on red blood cells and the targeted upstream delivery to different target organs in mice, pigs and ex vivo human lungs.

Mounting evidence suggests that d-amino acids play previously underappreciated roles in diverse organisms. In bacteria, even d-amino acids that are absent from canonical peptidoglycan (PG) may act as growth substrates, as signals, or in other functions. Given these proposed roles and the ubiquity of d-amino acids, the paucity of known d-amino-acid-responsive transcriptional control mechanisms in bacteria suggests that such regulation awaits discovery. We found that DarR, a LysR-type transcriptional regulator (LTTR), activates transcription in response to d-Asp. The d-Glu auxotrophy of a Vibrio fischeri murI::Tn mutant was suppressed, with the wild-type PG structure maintained, by a point mutation in darR. This darR mutation resulted in the overexpression of an adjacent operon encoding a putative aspartate racemase, RacD, which compensated for the loss of the glutamate racemase encoded by murI. Using transcriptional reporters, we found that wild-type DarR activated racD transcription in response to exogenous d-Asp but not upon the addition of l-Asp, l-Glu, or d-Glu. A DNA sequence typical of LTTR-binding sites was identified between darR and the divergently oriented racD operon, and scrambling this sequence eliminated activation of the reporter in response to d-Asp. In several proteobacteria, genes encoding LTTRs similar to DarR are linked to genes with predicted roles in d- and/or l-Asp metabolism. To test the functional similarities in another bacterium, darR and racD mutants were also generated in Acinetobacter baylyi. In V. fischeri and A. baylyi, growth on d-Asp required the presence of both darR and racD. Our results suggest that multiple bacteria have the ability to sense and respond to d-Asp.

IMPORTANCE d-Amino acids are prevalent in the environment and are generated by organisms from all domains of life. Although some biological roles for d-amino acids are understood, in other cases, their functions remain uncertain. Given the ubiquity of d-amino acids, it seems likely that bacteria will initiate transcriptional responses to them. Elucidating d-amino acid-responsive regulators along with the genes they control will help uncover bacterial uses of d-amino acids. Here, we report the discovery of DarR, a novel LTTR in V. fischeri that mediates a transcriptional response to environmental d-Asp and underpins the catabolism of d-Asp. DarR represents the founding member of a group of bacterial homologs that we hypothesize control aspects of aspartate metabolism in response to d-Asp and/or to d-Asp-containing peptides.

Angewandte Chemie International Edition, EarlyView.

Angewandte Chemie International Edition, EarlyView.

Martino et al. demonstrate that, in the symbiosis between Drosophila and Lactobacillus plantarum, the host diet represents the driving force in the evolution of L. plantarum symbiotic effect. This is a clear example of by-product mutualism, where the host capitalizes on the by-products of the self-serving traits of their symbionts.

Glutamic acid–valine–citrulline linkers ensure stability and efficacy of antibody–drug conjugates in mice

Glutamic acid–valine–citrulline linkers ensure stability and efficacy of antibody–drug conjugates in mice, Published online: 28 June 2018; doi:10.1038/s41467-018-04982-3

The valine-citrulline dipeptide, which is used as a cleavable linker for antibody-drug conjugates, is instable in mouse plasma. Here, the authors developed a glutamic acid–valine–citrulline tripeptide sequence as a stable alternative that still is susceptible to cathepsin-mediated cleavage.

ChemBioChem, Volume 19, Issue 16, Page 1766-1770, August 16, 2018.

Matlung et al. identify trogoptosis as an immune cell-mediated mechanism of cytotoxicity, demonstrating that neutrophil-mediated destruction of antibody-opsonized cancer cells occurs through a specific process that is distinct from that used by other immune cells.

Bacterial biofilms efficiently evade immune defenses, greatly complicating the prognosis of chronic infections. How methicillin-resistant Staphylococcus aureus (MRSA) biofilms evade host immune defenses is largely unknown. This study describes some of the major mechanisms required for S. aureus biofilms to evade the innate immune response and provides evidence of key...

Revealing the immune perturbation of black phosphorus nanomaterials to macrophages by understanding the protein corona

Revealing the immune perturbation of black phosphorus nanomaterials to macrophages by understanding the protein corona, Published online: 26 June 2018; doi:10.1038/s41467-018-04873-7

The formation of a protein corona around nanomaterials is known to have significant effects upon materials in biological applications. Here, the authors report on a study into understanding the protein corona formed on black phosphorus and the implications for interactions with macrophages.

Chlamydia trachomatis paralyses neutrophils to evade the host innate immune response

<i>Chlamydia trachomatis</i> paralyses neutrophils to evade the host innate immune response, Published online: 25 June 2018; doi:10.1038/s41564-018-0182-y

Chlamydia trachomatis-secreted protease CPAF cleaves FPR2 to subvert neutrophil activation and escape immune control.

by Daniel Pletzer, Sarah C. Mansour, Robert E. W. Hancock

With the antibiotic development pipeline running dry, many fear that we might soon run out of treatment options. High-density infections are particularly difficult to treat due to their adaptive multidrug-resistance and currently there are no therapies that adequately address this important issue. Here, a large-scale in vivo study was performed to enhance the activity of antibiotics to treat high-density infections caused by multidrug-resistant Gram-positive and Gram-negative bacteria. It was shown that synthetic peptides can be used in conjunction with the antibiotics ciprofloxacin, meropenem, erythromycin, gentamicin, and vancomycin to improve the treatment outcome of murine cutaneous abscesses caused by clinical hard-to-treat pathogens including all ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae) pathogens and Escherichia coli. Promisingly, combination treatment often showed synergistic effects that significantly reduced abscess sizes and/or improved clearance of bacterial isolates from the infection site, regardless of the antibiotic mode of action. In vitro data suggest that the mechanisms of peptide action in vivo include enhancement of antibiotic penetration and potential disruption of the stringent stress response.

It is commonly assumed that recognition and discrimination of chirality, both in nature and in artificial systems, depend solely on spatial effects. However, recent studies have suggested that charge redistribution in chiral molecules manifests an enantiospecific preference in electron spin orientation. We therefore reasoned that the induced spin polarization may affect enantiorecognition through exchange interactions. Here we show experimentally that the interaction of chiral molecules with a perpendicularly magnetized substrate is enantiospecific. Thus, one enantiomer adsorbs preferentially when the magnetic dipole is pointing up, whereas the other adsorbs faster for the opposite alignment of the magnetization. The interaction is not controlled by the magnetic field per se, but rather by the electron spin orientations, and opens prospects for a distinct approach to enantiomeric separations.

Encapsulated mammalian cells with a synthetic gene circuit to sense and respond to MRSA infection could provide potential prophylactic, diagnostic, or therapeutic options for medical implant-associated infections.

Ablating the histone demethylase LSD1 genetically or pharmacologically enhances tumor immunogenicity by stimulating endogenous retrovirus expression and downregulating RNA-induced silencing complex, supporting the promise of LSD1 inhibition in overcoming resistance to checkpoint blockade in cancer treatment.

Angewandte Chemie International Edition, EarlyView.

by Abigail L. Reens, Amy L. Crooks, Chih-Chia Su, Toni A. Nagy, David L. Reens, Jessica D. Podoll, Madeline E. Edwards, Edward W. Yu, Corrella S. Detweiler

Bacterial efflux pumps transport small molecules from the cytoplasm or periplasm outside the cell. Efflux pump activity is typically increased in multi-drug resistant (MDR) pathogens; chemicals that inhibit efflux pumps may have potential for antibiotic development. Using an in-cell screen, we identified three efflux pump modulators (EPMs) from a drug diversity library. The screening platform uses macrophages infected with the human Gram-negative pathogen Salmonella enterica (Salmonella) to identify small molecules that prevent bacterial replication or survival within the host environment. A secondary screen for hit compounds that increase the accumulation of an efflux pump substrate, Hoechst 33342, identified three small molecules with activity comparable to the known efflux pump inhibitor PAβN (Phe-Arg β-naphthylamide). The three putative EPMs demonstrated significant antibacterial activity against Salmonella within primary and cell culture macrophages and within a human epithelial cell line. Unlike traditional antibiotics, the three compounds did not inhibit bacterial growth in standard microbiological media. The three compounds prevented energy-dependent efflux pump activity in Salmonella and bound the AcrB subunit of the AcrAB-TolC efflux system with K_Ds in the micromolar range. Moreover, the EPMs display antibacterial synergy with antimicrobial peptides, a class of host innate immune defense molecules present in body fluids and cells. The EPMs also had synergistic activity with antibiotics exported by AcrAB-TolC in broth and in macrophages and inhibited efflux pump activity in MDR Gram-negative ESKAPE clinical isolates. Thus, an in-cell screening approach identified EPMs that synergize with innate immunity to kill bacteria and have potential for development as adjuvants to antibiotics.