The cervicovaginal microbiome of pregnant people living with HIV on antiretroviral therapy in the Democratic Republic of Congo: A Pilot Study and Global Meta-analysis.

Unlabelled: Recent studies are revealing that a suboptimal cervicovaginal microbiome (CVMB), including enrichment of anaerobic bacteria associated with multiple female genital disorders, and adverse pregnancy and birth outcomes in pregnant people. Problematically, however, the majority of the available data to date are biased towards highly developed, Global North countries, leaving underrepresented populations like the Democratic Republic of Congo (DRC) poorly characterised. Here, we investigate the CVMB from a cohort of 82 pregnant people living with HIV (PLWH) on antiretroviral therapy (ART) from the DRC.

Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.

Microbes drive ecosystem function through their physical interactions and metabolic transformations. However, since microbiomes are ecologically and metabolically interconnected, it is challenging to predict emergent ecosystem responses once the microbiome is disturbed. While it is widely acknowledged that mammalian gut dysbiosis influences host metabolism, mechanistic links that predict these effects are understudied.

Virocell resource manipulation under nutrient limitation.

Virus-infected cells, called virocells, impact host metabolic functions, resources, and ecosystem processes, but the effects of nutrient limitation remain less well understood. Here, we leverage transcriptomic, proteomic, and endo- and exo-metabolomic data from two virocells independently infected by unrelated dsDNA viruses, PSA-HS2 (HS2-virocells) and PSA-HP1 (HP1-virocells), to examine how phosphate limitation affects virocell resource manipulation intra- and extracellularly. Intracellularly, we find that (i) HP1-virocells boost amino acid production toward the end of the infection cycle but deplete amino acid pools relative to HS2-virocells; (ii) both virocells dampen the production of nucleotide synthesis proteins; (iii) HS2-virocells switch from synthesis to recycling of phospholipids, whereas HP1-virocells decrease both activities; (iv) all cells (virocells and uninfected cells), but HP1-virocells especially, increase membrane fluidity; and (v) both virocells increase iron storage.

Disruption of The Spinal Cord-Gut Axis Alters Gut Microbial Dynamics and Carbohydrate Cross-feeding.

The spinal cord, a nexus for brain-body crosstalk, controls gut physiology and microbial homeostasis, but the underlying mechanisms remain unclear. Using genome-resolved longitudinal metagenomics in male and female C57BL/6 mice before and up to 6 months after disrupting the spinal cord-gut axis, we reconstructed over 6,500 microbial draft genomes. This "Mouse B6 Gut Catalog" improved or doubled species- and strain-level representation in other published catalogs.

Polyphenol rewiring of the microbiome reduces methane emissions.

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, ~40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems.

Unveiling plasmid diversity and functionality in pristine groundwater.

Background: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

Results: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids.

Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.

Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard.

Infection and Genomic Properties of Single- and Double-Stranded DNA Phages.

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages-ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.

Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics.

Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.

A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.

Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning.

Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.

Microbiomes influence diverse ecosystems, but viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least nine studies.

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al.

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp.

A functional microbiome catalogue crowdsourced from North American rivers.

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb).

Polyphenol rewiring of the microbiome reduces methane emissions.

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens, either through direct toxic effects or by diverting their substrates and energy, to gain traction. Problematically, current microbial methane mitigation knowledge derives from rumen studies and lacks detailed microbiome-centered insights, limiting translation across ecosystems.

Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.

Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures.

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals.

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs.

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.

Background: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.

Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats.

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle.

With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch.

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths.

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific mAs.

Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods.

Environment-specific virocell metabolic reprogramming.

Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood.

Viral potential to modulate microbial methane metabolism varies by habitat.

Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways.

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale.

Interrogating the viral dark matter of the rumen ecosystem with a global virome database.

The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3.