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Phages are viruses that prey on bacteria for reproduction, which typically results in the lysing of the bacterial host cell.
Bacteriophages are the most common biological entities on Earth. They play important roles in influencing microbial communities. Most phages either destroy bacteria (lytic) or become part of the bacteria's DNA (prophages), creating a bacterial lysogen. Studies of certain integrated phages, like λ and Mu, have helped us understand lysogens and have been key to molecular biology.
Bacteriophages and other mobile genetic elements (MGEs) pose a constant threat to bacteria. In response, bacteria have developed an immune system employing various strategies to defend themselves. Interestingly, evidence suggests that many of these defense mechanisms originate from MGEs themselves, challenging our traditional understanding of bacterial immunity and raising intriguing questions about evolutionary processes. The distribution of these defense systems within bacterial genomes is intricately linked to ecological and evolutionary interactions with MGEs.
Bacteriophages are key components of gut microbiota .
They are highly abundant in the human gut, yet most remain uncultured. Here, we present a gut phage isolate collection (GPIC) containing 209 phages for 42 commensal human gut bacterial species. Genome analysis of the phages identified 34 undescribed genera
Shen et al. 2023 Cell Host & Microbe 31(4): 665-677
In the adult human gut, it is estimated that phages and bacteria exist in an about 1:1 ratio, although the actual number can be potentially higher (i.e., in the mucus layer).
Determining which hosts a phage can infect is crucial for several reasons. It aids in the application of phages for therapeutic purposes, helps control bacterial populations, and manages their impact on various processes. Traditionally, the host range of phages is assessed by observing their ability to lyse host cells. However, the molecular mechanisms underlying this process are often overlooked. Phages attach to bacteria primarily through specific proteins, which was once considered the primary determinant of host specificity. Recent insights reveal that the interaction is more intricate.
Infection assays showed that Bacteroides and Parabacteroides phages are specific to a bacterial species, and strains of the same species exhibit substantial variations in phage susceptibility
Shen et al. 2023 Cell Host & Microbe 31(4): 665-677
A cocktail of 8 phages with a broad host range for Bacteroides fragilis strains effectively reduced their abundance in complex host-derived communities in vitro
Shen et al. 2023 Cell Host & Microbe 31(4): 665-677
Proof-of-concept assessment of Klebsiella pneumoniae strains-targeting phages in an artificial human gut and in healthy volunteers demonstrate gastric acid-dependent phage resilience, safety, and viability in the lower gut. We demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance while effectively inhibiting non-communicable disease (Inflammatory Bowel Disease (IBD))-contributing pathobionts.
The infant gut microbiota follows a defined successional pattern where both bacterial and phage communities evolve over time. The initial phage colonizers in the infant gut seem primarily derived from induced prophages of pioneering gut bacteria, obtained from environmental sources such as the birth canal, maternal gut microbiome, or from breastfeeding.
Approximately 9% of early phage colonizers, mostly maternally transmitted and infecting Bacteroides, persisted for three years. These persistent phages were more likely to be found in infants with a higher diversity of gut microbiota.
Stop codon reassignments and mutations in the tail fiber genes of bacteriophages may play a significant role in facilitating stable viral colonization in the gut environment. These genetic adaptations could be crucial for the phages to establish and maintain a presence within the complex ecosystem of the gut microbiome.