The increasing interest in the human microbiota raises some interesting questions about the terminology we use to describe some of the structures and strategies employed by commensal and pathogenic ...microbes to compete in these complex biological ecosystems. For example, all microbes arriving in the alimentary tract face the task of surviving passage through the stomach, coping with bile, interacting with the immune system, competing with the established microbiota, and obtaining sufficient nutrients to gain a foothold in this hostile environment. It is not surprising then that many gastrointestinal microbes (both pathogens and commensals) use similar strategies to overcome the challenges associated with this particular biological niche. Given that many of these structures and strategies were discovered and characterized in pathogens and because they often play important roles in establishing and maintaining an infection, they have often been characterized as virulence factors. It would be misleading to describe the same strategies and structures found in harmless commensals as “virulence factors,” since they represent a sine qua non for life in the gastrointestinal tract. It may be time to reconsider and refer to them as “niche factors,” both in terms of providing scientific accuracy but also in light of the growing interest in using gut microbes as probiotics, where the distinction between virulence factors and niche factors is likely to be very important from a regulatory perspective.
The human gut microbiome is a dense and taxonomically diverse consortium of microorganisms. While the bacterial components of the microbiome have received considerable attention, comparatively little ...is known about the composition and physiological significance of human gut-associated bacteriophage populations (phageome). By extrapolating our knowledge of phage-host interactions from other environments, one could expect that >1012 viruses reside in the human gut, and we can predict that they play important roles in regulating the complex microbial networks operating in this habitat. Before delving into their function, we need to first overcome the challenges associated with studying and characterizing the phageome. In this Review, we summarize the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome. We also discuss the main challenges in the field and identify promising avenues for future research.
Shkoporov and Hill review our current understanding of and the available methods for studying the taxonomic composition, community structure, and population dynamics of human gut-associated bacteriophage populations (phageome). They also discuss the main challenges in the field and identify avenues for future research.
Nisin is a 34-amino-acid lantibiotic that has been used commercially for almost a century as a food preservative. In order to produce active nisin,
requires an 11-gene operon that encodes proteins ...involved in modification, processing, transport, immunity, and regulation. While the role of each of the 11 proteins is well understood, the location and spatial organization of the biosynthetic machinery that involves NisA, NisB, NisC, NisT, and NisP remain to be determined. In this elegant paper (J. Chen, A. J. van Heel, and O. P. Kuipers, mBio 11:e02825-20, 2020, https://doi.org/10.1128/mBio.02825-20), we learn that a NisB dimer is recruited to the "old" pole of a dividing cell, where it assembles with NisC to form a modification complex that can engage with NisA. Unexpectedly, the NisT transporter does not stably assemble into this complex but is distributed around the membrane until it engages with the NisABC complex to transport NisA across the membrane, whereupon it dissociates from NisBC.
Abstract Recent measurements of Galactic polarized dust emission have found a nonzero TB signal, a correlation between the total intensity and the B -mode polarization component. We present evidence ...that this parity-odd signal is driven by the relative geometry of the magnetic field and the filamentary interstellar medium in projection. Using neutral hydrogen morphology and Planck polarization data, we find that the angle between intensity structures and the plane-of-sky magnetic field orientation is predictive of the signs of Galactic TB and EB . Our results suggest that magnetically misaligned filamentary dust structures introduce nonzero TB and EB correlations in the dust polarization, and that the intrinsic dust EB can be predicted from measurements of dust TB and TE over the same sky mask. We predict correlations between TE , TB , EB , and EE / BB , and confirm our predictions using synthetic dust polarization maps from magnetohydrodynamic simulations. We introduce and measure a scale-dependent effective magnetic misalignment angle, ψ ℓ dust ∼ 5 ° for 100 ≲ ℓ ≲ 500, and predict a positive intrinsic dust EB with amplitude D ℓ EB ≲ 2.5 μ K CMB 2 for the same multipole range at 353 GHz over our sky mask. Both the sign and amplitude of the Galactic EB signal can change with the sky area considered. Our results imply that searches for parity violation in the cosmic microwave background must account for the nonzero Galactic EB and TB signals, necessitating revision of existing analyses of the evidence for cosmic birefringence.
Solutions are urgently required for the growing number of infections caused by antibiotic-resistant bacteria. Bacteriocins, which are antimicrobial peptides produced by certain bacteria, might ...warrant serious consideration as alternatives to traditional antibiotics. These molecules exhibit significant potency against other bacteria (including antibiotic-resistant strains), are stable and can have narrow or broad activity spectra. Bacteriocins can even be produced in situ in the gut by probiotic bacteria to combat intestinal infections. Although the application of specific bacteriocins might be curtailed by the development of resistance, an understanding of the mechanisms by which such resistance could emerge will enable researchers to develop strategies to minimize this potential problem.
The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of ...human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as "viral dark matter." Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform
phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.
Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new ...environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops.
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