The genus Pseudomonas is one of the most versatile groups of bacteria known to science. First defined in 1894 by the German mycologist Walter Migula, it comprises Gram-negative, aerobic, rod-shaped bacteria equipped with flagella. Over more than a century of microbiological discovery, the genus has grown to encompass 381 validly published species, according to the List of Prokaryotic names with Standing in Nomenclature, with Pseudomonas aeruginosa serving as the type species. Members of the genus colonize soil, rivers, plants and animal hosts, and their roles range from promoting plant growth and cleaning contaminated environments to causing serious opportunistic infections in vulnerable patients. Among the many niches these bacteria occupy is human milk, a biological fluid whose microbial community helps seed the newborn gut and shapes early immune and metabolic development.

Despite the growing interest in the milk microbiome, African populations remain markedly under-studied, and most surveys of milk bacteria rely on culture-independent methods that detect genetic signatures without ever yielding a living isolate. Motivated by this gap, the research team turned to a culture-based, genome-resolved strategy. Breast milk samples were collected from mothers of both malnourished and healthy children in Niakhar, Senegal, with informed consent and approval from the Ethical and Scientific Committee of the Senegalese Ministry of Health and Public Hygiene. Ten to fifteen milliliters of milk from each participant were transported at four degrees Celsius to a laboratory in Dakar, aliquoted, frozen at minus eighty degrees Celsius, and later shipped on dry ice to Marseille for culturing, sequencing and analysis.

Two strains, designated Marseille-QA0332 and Marseille-QA0892, emerged from this effort. The first was obtained by direct plating of milk onto Columbia blood agar during routine colony counting, before any enrichment step. The second was recovered through a culturomics protocol, in which milk was inoculated into a series of liquid enrichment media and subcultured at scheduled intervals over thirty days; strain QA0892 appeared at the day-fifteen subculture from an aerobic blood-culture bottle containing MacConkey broth. Rigorous sterility controls, in which every batch of medium was tested for contamination before use, ensured that any bacterial growth traced back to the milk samples themselves rather than to laboratory reagents.

Initial identification attempts using MALDI-TOF mass spectrometry failed to match either isolate to a known species, prompting whole-genome sequencing. Comparison of 16S ribosomal RNA gene sequences showed that strain QA0332 shared its highest similarity, 97.98 percent, with Pseudomonas ceruminis, while strain QA0892 was 99 percent similar to Pseudomonas matsuisoli. Those figures alone might have suggested close relatives, but whole-genome comparisons told a different story. Average nucleotide identity values, which should exceed roughly 95 to 96 percent between strains of the same species, came in at just 81.1 to 81.4 percent for QA0332 against its nearest neighbors and 75.0 percent for QA0892 against P. matsuisoli. Digital DNA-DNA hybridization values, with a species threshold of 70 percent, were even lower, at 26.7 percent and 21.1 percent respectively. By every genomic yardstick, the two isolates represented lineages distinct from any previously described species.

The phenotypic portraits of the two bacteria are strikingly different. Pseudomonas senegalensis grows optimally at 37 degrees Celsius under aerobic conditions and forms circular, convex, yellowish, mucoid colonies. It is motile, non-spore-forming, oxidase- and catalase-positive, and capable of fermenting a broad range of sugars including glucose, xylose, arabinose and trehalose. It also produces urease and arginine dihydrolase, traits that help distinguish it from close relatives. Pseudomonas millioni, by contrast, prefers cooler temperatures, growing best at room temperature and 28 degrees Celsius in alkaline media, and its colonies mature from translucent punctiform dots into dry, filamentous, opaque mats. Uniquely among its comparisons, it reduces nitrate to nitrite and hydrolyzes esculin. Fatty acid profiling by gas chromatography further separated the two: the cell membranes of P. senegalensis are dominated by hexadecanoic acid and cis-9,10-methylene-hexadecanoic acid, while those of P. millioni feature a more balanced mixture of unsaturated and saturated fatty acids.

Genome architecture reinforced the case for two new species. Pseudomonas senegalensis carries a single circular chromosome of 4,577,173 base pairs with a GC content of 63.65 percent, encoding 4,173 genes, of which 4,079 are protein-coding. Pseudomonas millioni has a slightly larger chromosome of 4,658,126 base pairs, a GC content of 60.22 percent, and 4,327 genes. Neither genome contains plasmids, and functional annotation revealed repertoires dominated by amino acid transport, transcription, energy production and inorganic ion metabolism, consistent with metabolically versatile, free-living organisms. Mining of secondary metabolite biosynthetic gene clusters uncovered eleven candidate regions in P. senegalensis and eight in P. millioni, including a pseudomonine-like metallophore cluster in the former, suggesting a siderophore-based iron-scavenging system well suited to the iron-limited environment of milk. Both genomes also harbor carotenoid, hydrogen cyanide and N-acetylglutaminylglutamine amide clusters, although the researchers caution that these remain computational predictions rather than chemically validated products.

From a clinical standpoint, the news is reassuring. Screening against virulence factor databases found none of the hallmark weapons of Pseudomonas aeruginosa: no type III secretion system, no exotoxin A, no elastase or phospholipases, and no high-risk pathogenicity islands. No acquired resistance genes, such as extended-spectrum beta-lactamases or carbapenemases, were detected in either genome. The only resistance determinants identified were intrinsic chromosomal efflux pumps and regulators typical of the genus. One notable exception emerged in Pseudomonas millioni, which proved resistant to the antibiotic ceftazidime. A targeted search revealed a chromosomal class C beta-lactamase, bearing the three canonical catalytic motifs of Ambler class C enzymes, that accounts for this phenotype. Because the enzyme is intrinsic and not transmissible, the researchers conclude that both species pose a low biosafety risk, though they note that pathogenic potential cannot be formally excluded without infection models.

Perhaps the most intriguing evidence for the ecological identity of these bacteria comes from mining public metagenomic archives through the IMNGS platform. Both species were detected predominantly in human-associated ecosystems rather than environmental ones. Pseudomonas senegalensis appeared in 0.95 percent of human gut metagenomes and 0.69 percent of skin metagenomes, while Pseudomonas millioni was found in 1.53 percent of gut metagenomes and 0.50 percent of blood metagenomes. This pattern of low prevalence but consistent human association supports the idea that the two organisms are genuine members of the human microbiome rather than transient contaminants. The researchers argue that the combination of viable cultured isolates, verified sterile media and expected recovery of Pseudomonas from milk makes a laboratory origin for the strains implausible.

The discovery also carries a cautionary lesson about genome-based inference. Both genomes encode a carotenoid biosynthetic cluster, yet only Pseudomonas senegalensis forms visibly yellow colonies. This dissociation between genotype and phenotype demonstrates that the mere presence of a biosynthetic gene cluster does not guarantee its expression, tempering the functional conclusions that can be drawn from genome mining alone. With type strains deposited in the Collection de Souches de l’Unité des Rickettsies in Marseille and the Colección Española de Cultivos Tipo in Spain, and genome sequences available in GenBank, Pseudomonas senegalensis and Pseudomonas millioni now stand as formally recognized members of the bacterial tree of life, and as reminders of how much microbial diversity still hides in ordinary human fluids waiting to be cultured.

Subject of Research: Discovery and taxonomic description of two novel Pseudomonas species isolated from human breast milk in Senegal

Article Title: Pseudomonas senegalensis sp. nov. and Pseudomonas millioni sp. nov., two novel species isolated from the breast milk of Senegalese women

Article References: Pseudomonas senegalensis sp. nov. and Pseudomonas millioni sp. nov., two novel species isolated from the breast milk of Senegalese women. (n.d.). https://doi.org/10.1016/j.nmni.2026.101846

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101846

Keywords: Pseudomonas senegalensis, Pseudomonas millioni, breast milk microbiota, new bacterial species, taxonogenomics, Senegal, culturomics, whole-genome sequencing, antimicrobial resistance, human microbiome, MALDI-TOF, New Microbes and New Infections

The article, led by Carl Folke of the Anthropocene Laboratory at the Royal Swedish Academy of Sciences and co-authored by an international team spanning ecology, microbiology, hydrology, economics and the arts, argues that the notion of ‘people and nature’ being intertwined is not merely a philosophical or ethical stance. It is a hard biochemical reality. The human body, the authors contend, is an open living system in continuous exchange with the chemical elements of the Earth, and the movement of those elements into and out of our bodies is mediated at every step by living organisms: bacteria, fungi, plants, plankton, insects, birds, fish and mammals. To be alive, in the most literal sense, is to be threaded through with the web of life.

The evidence begins with the periodic table itself. The human body contains at least sixty detectable chemical elements, of which roughly twenty are essential for basic metabolism. Six elements—oxygen, hydrogen, nitrogen, carbon, calcium and phosphorus—constitute ninety-nine percent of body mass, forming the scaffolding of bones, tissues and cells. Five more—sulphur, potassium, sodium, chlorine and magnesium—are critical for nerve conduction, muscle contraction and fluid balance. Trace elements such as iron, zinc, copper, iodine, selenium and cobalt act as cofactors in enzymes, enable oxygen transport, support immune defence and drive DNA transcription. Crucially, the body cannot manufacture any of these from scratch; they must be acquired from external sources, which means from the biosphere.

But the acquisition is rarely direct, and this is where the paper’s technical depth becomes remarkable. Consider the gut microbiome. Over half the cells in a healthy human body belong to microbes, and these communities perform functions integral to whole-organism health. The gut is dominated by obligate anaerobic bacteria whose metabolisms mirror those of Earth’s earliest life forms, which emerged some 3.7 billion years ago in oxygen-poor environments using sulphur and nitrate as electron acceptors. In our large intestine today, their descendants ferment dietary fibre into short-chain fatty acids such as butyrate, a primary energy source for intestinal epithelial cells and a signalling molecule in the gut-brain axis. These metabolites influence immune responses, hypothalamic–pituitary–adrenal axis activity and even the synthesis of serotonin. In parallel, gut microbes synthesise B vitamins—including up to thirty-seven percent of a healthy adult’s daily folate requirement—and mediate the bioavailability of minerals such as calcium, magnesium, iron and phosphorus, competing with our own cells for limiting metals in a dynamic the authors call the human-microbiome-element symbiosis.

Extending outward, the paper traces how planetary-scale biogeochemical cycles deliver those essential elements to the human body through air, water and food. Roughly half of the oxygen in every breath is produced by oceanic photosynthesis, much of it by microscopic phytoplankton such as diatoms and the cyanobacterium Prochlorococcus marinus, a single species responsible for as much as five percent of global photosynthesis. On land, tropical forests account for about thirty-four percent of terrestrial oxygen production. Yet the authors stress that current biomes collectively produce and consume approximately the same amount of oxygen, meaning today’s atmospheric oxygen is a legacy of geological burial processes, predominantly in the ocean, accumulated over millions of years. In this sense, humanity is entangled not only with contemporary ecosystems but with the metabolic work of life across deep time.

Water, described by the authors as the ‘flowing bloodstream’ of the biosphere, offers another vivid illustration. Humans require a continuous turnover of one to six litres of water daily, and the patterns of freshwater circulation that make this possible are not simply physical. Terrestrial ecosystems store soil moisture, sustain evaporation and generate downwind rainfall. Around forty to fifty percent of precipitation over land is recycled by evapotranspiration from plants and soil, and a barren planet would generate less than a third of that moisture flux. The freshwater we drink dissolves calcium, magnesium and iron from rocks and soils, delivering them into the body. Meanwhile, food production depends on even larger volumes of green water: an adequate daily diet requires three thousand to four thousand litres of evapotranspiration per person, with croplands in as many as 155 countries receiving up to forty percent of their annual precipitation from forests located in other nations through atmospheric moisture transport.

Soil and marine ecosystems complete the picture. Soil organisms, representing nearly sixty percent of Earth’s species, decompose organic matter and mineralise bound nutrients into plant-available forms. A single gram of soil can contain up to ten billion microorganisms. Earthworms deepen rooting zones, nematodes stimulate bacterial mineralisation, and mycorrhizal fungi extend the foraging reach of plant roots through hyphal networks, trading soil nutrients for plant sugars in a mutualism stabilised by reciprocal rewards. Because our DNA depends on phosphorus, and most plants require mycorrhizal fungi to acquire it, a substantial portion of the phosphorus in human genetic material has likely passed through a fungal network. In the ocean, upwelling systems supply trace metals that constrain marine productivity, and seafood acts as a concentrated route through which marine biogeochemistry becomes human micronutrition—iodine from seaweed and fish, selenium and omega-3 fatty acids concentrated through trophic levels.

Animals also function as what ecologists call ‘mobile links’, redistributing nutrients across landscapes and ecosystems in ways that directly affect human food security. Baleen whales recycle iron into surface waters, supporting phytoplankton blooms. Seabird guano transfers between ten thousand and one hundred thousand tonnes of phosphorus to land each year, and in Greenland the guano of thirty-three million pairs of little auks fertilises soils that sustain hares, geese, foxes, reindeer and muskoxen relied upon by local human communities. Salmon returning from the sea carry marine-derived nutrients into freshwater and forests, while insect pollinators were found to be directly responsible for more than twenty percent of vitamin A, folate and vitamin E intake in vulnerable smallholder communities in Nepal.

Against this backdrop, the paper delivers a stark warning about the Anthropocene. Human activity—industrialisation, fossil-fuel combustion, synthetic fertiliser use, monoculture farming, pesticide application and the proliferation of novel entities such as plastics and PFAS—is reshuffling the life-element relationships upon which human bodies depend. Soil micronutrient deficiencies are spreading, marine fish biomass and their cycling rates have been nearly halved by fisheries, and microbial communities are being compositionally and functionally altered by antibiotics, urban infrastructure and intensified agriculture. Eighty percent of people in low-income countries now live with degraded land, unhealthy air and water stress. Six of nine planetary boundaries have been exceeded, and the technosphere—the sum of human-made material—has, as of 2020, exceeded the dry weight of all living biomass on Earth. Yet none of this, the authors insist, implies independence. It implies disruption.

The synthesis concludes with a call for what the authors term ‘stewardship of life-element mediation’: a form of biosphere stewardship that is not merely cognitive or ethical but embodied—a set of lived practices and institutions that sustain the living relations making human existence materially possible. They point to emerging domains such as microbiome health, agroecology, rewilding, marine protected areas and nature-based solutions as evidence of a growing practical knowledge base that works with living mediators of elemental flow rather than treating food, water, health and biodiversity as separate concerns. Being human, the authors argue, means being an open system threaded through with bacteria, fungi, plants, plankton, birds, whales and the chemical elements they mobilise. Life keeps us alive. Recognising this as a biogeochemical fact, rather than a metaphor, may be among the most consequential scientific reframings of our time.

Subject of Research: The biochemistry of human interdependence with life-mediated chemical element cycles in the Anthropocene biosphere

Article Title: Humans: Intertwined with life and the basic elements in the Anthropocene biosphere

Article References: Humans: Intertwined with life and the basic elements in the Anthropocene biosphere. (n.d.). https://doi.org/10.1007/s13280-026-02474-z

Image Credits: AI Generated

DOI: 10.1007/s13280-026-02474-z

Keywords: Anthropocene, biosphere, biogeochemical cycles, human microbiome, gut-brain axis, photosynthesis, water cycle, soil health, mycorrhizal fungi, phytoplankton, planetary boundaries, biosphere stewardship