To successfully tackle the current mpox public-health emergency, we must learn from past outbreaks to focus research questions and take collaborative action.

In this Review, the authors discuss fungal pathogen–host interactions with a focus on phagocytosis and intracellular processing of pathogens within phagosomes. They also outline potential therapeutic approaches for targeting intraphagosomal pathogens.

A multi-omics analysis of oncom, an Indonesian fermented food made from soymilk waste, shows how associated fungi break down food waste to yield nutritious and positively received foods.

Primary colonization by microbial communities dominated by Bifidobacteria contribute to stable gut microbiota assembly and long-term pathogen resistance in neonates.

Bismuth-based drugs combined with antibiotics enhance efficacy against multidrug-resistant Pseudomonas aeruginosa by disrupting bacterial iron homeostasis and electron transport.

RoseTTAFold2-Lite uses residue–residue coevolution and protein structure prediction to identify and structurally characterize protein–protein interactions in bacterial pathogens.

A microbially derived bile acid, taurolithocholic acid, limits viral replication, host inflammation and ferroptosis during infection with severe fever with thrombocytopenia syndrome virus, an emerging tick-borne haemorrhagic fever virus.

Sulfated glycosaminoglycans are host cell targets of candidalysin, a cytolytic toxin of the fungal pathogen Candida albicans.

Endothelin-1 activation after SARS-CoV-2 infection leads to vascular permeability, chondrocyte senescence, osteoclast activation and cyst formation in affected joints of hamsters, which can be alleviated using macitentan. Joint injury was also seen in two patients after COVID-19 infection.

Primary colonization by microbial communities dominated by Bifidobacteria contribute to stable gut microbiota assembly and long-term pathogen resistance in neonates.

Thomas Mettenleiter was president of the Friedrich-Loeffler-Institut for 27 years and retired in June 2023. Looking back, he reflects on events around and following the reunification of Germany that changed his career path.

Julie Chih-yu Chen is the head of Data Sciences at the National Microbiology Laboratory, Public Health Agency of Canada, and an Assistant Professor at the University of Manitoba, Canada. She develops and applies statistical and machine learning techniques to diverse omics data related to infectious disease.

Persistence of the transcriptionally active HIV reservoir has important implications for people living with HIV, including chronic immune activation and inflammation. Supplementing antiretroviral therapy with transcriptional inhibitors could overcome this by silencing the transcriptionally active HIV reservoir.

To successfully tackle the current mpox public-health emergency, we must learn from past outbreaks to focus research questions and take collaborative action.

Moving from academia to government was challenging, but learning to translate evidence-based results into policy decisions that impact society is hugely rewarding, writes Robin May.

This month’s issue of Nature Microbiology has a focus on microbial ecology, showcasing how these dynamics might be harnessed to better understand and safeguard life on Earth.