Poultry Litter Reshapes Soil Bacteria in Lagos Farms, Raising Pathogen Concerns

On the outskirts of Lagos, in the peri-urban district of Ikorodu, the ground beneath two working poultry farms is telling a story that scientists say should change how the world thinks about organic fertilizer. A team of Nigerian researchers, led by Abraham Ajayi of the Nigerian Institute of Medical Research and published in BMC Environmental Science, has used high-throughput DNA sequencing to reveal that poultry litter, the mixture of droppings and decomposing bedding that accumulates in chicken houses, does far more than enrich soil with nutrients. It fundamentally rewrites the bacterial communities living in the earth below, replacing the typical soil microbiome with a microbial signature that looks strikingly like the inside of a chicken gut, and introducing bacteria with documented links to human disease.

The study set out to answer a deceptively simple question: what does poultry farming actually do to the microscopic life in soil? The researchers collected composite soil samples from two farms within a poultry estate in Ikorodu, designated PF01A and PF02B, and compared them with soil from a pristine control site, labeled CTR, that had no history of farming activity. Using a soil auger, they sampled five points at each location, sieved the material to create composite samples, and transported everything at four degrees Celsius to the laboratory. Ethical and social approvals were secured from the Nigerian Institute of Medical Research and the Lagos State Ministry of Health before any sampling began.

The technical backbone of the study was metagenomic analysis of the bacterial 16S rRNA gene, specifically the V3 to V4 hypervariable regions, which act like molecular barcodes for identifying bacterial taxa. The team extracted total community DNA from half a gram of soil using a commercial soil kit, adding skim milk to the lysis matrix to prevent humic substances from interfering with the polymerase chain reaction. Sequencing was performed on an Illumina MiSeq platform, generating tens of millions of reads that were then quality filtered, merged, denoised, and clustered into operational taxonomic units, or OTUs, using a pipeline that included Trimmomatic, PANDAseq, DUDE-Seq, and UCHIME, with taxonomic assignments made against the EzBioCloud 16S database at a 97 percent similarity threshold.

The scale of the data was considerable. After quality filtering, the researchers obtained 17,714 valid bacterial reads from PF02B, 16,975 from PF01A, and 24,218 from the control site. The farm soils clustered into roughly 1,000 to 1,200 OTUs each, while the pristine soil contained 3,037 OTUs, indicating a far richer and more diverse native community. Good’s library coverage estimates exceeded 98 percent for both farm samples and reached 96 percent for the control, meaning the sequencing captured nearly the entire bacterial community at each site. Alpha diversity indices, including the Shannon and inverse Simpson measures, showed that PF01A hosted greater bacterial diversity than PF02B, but both were dramatically simplified compared with the untouched soil.

The most striking finding emerged at the phylum level. In the poultry-impacted soils, Firmicutes dominated overwhelmingly, accounting for 55 to 69 percent of reads, followed by Bacteroidetes at 18 to 19 percent and Actinobacteria at 3 to 17 percent, while Proteobacteria languished at around 7 percent. The control soil told the opposite story: Proteobacteria led at 30 percent, with Firmicutes at 28 percent, Actinobacteria at 22 percent, and a suite of other phyla, including Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadetes, and Nitrospirae, each contributing smaller shares. Bacteroidetes, a dominant group in the farm soils, barely registered at 2 percent in the pristine site. This inversion matters because Proteobacteria dominance is the expected pattern in healthy, nutrient-rich soils, so its displacement by Firmicutes and Bacteroidetes is a clear fingerprint of poultry litter.

The explanation, the researchers argue, lies in the origin of the litter itself. Firmicutes and Bacteroidetes are the dominant phyla in the duodenum, ileum, and cecum of chickens, so soil repeatedly receiving poultry droppings is essentially being inoculated with the gut microbiome of the birds. The authors note that the chicken gut microbiota is not stable and shifts with the age of the flock, which suggests the community profile observed in the soil may partly reflect the age of the birds that produced the litter. At the family level, the pattern held: Lactobacillaceae dominated both farm soils at 34.1 percent and 20.4 percent respectively, alongside Bacteroidaceae, Lachnospiraceae, Enterococcaceae, Corynebacteriaceae, Peptoniphilaceae, Planococcaceae, and Ruminococcaceae, while the control soil was led by Bacillaceae, Bradyrhizobiaceae, Gaiellaceae, and Sphingomonadaceae. None of the dominant families in the farm soils exceeded 1 percent abundance in the pristine soil, and heat map analysis confirmed that the two farm samples clustered together, clearly separated from the control.

Within those dominant taxa were species that give public health officials reason for concern. Corynebacterium xerosis, a bacterium implicated in ear infections, osteomyelitis, ventriculoperitoneal shunt infections, and brain abscesses, was among the dominant strains in both farm soils. So was Ignatzschineria indica, a Gram-negative bacillus associated with the parasitic flesh fly Wohlfahrtia magnifica and reported as a cause of bacteremia in patients with maggot-infested wounds. Its presence in poultry-litter soil is unsurprising, the authors note, because the odor of litter attracts swarms of flies. Other dominant organisms included Jeotgalibaca arthritidis, Lysinibacillus jejuensis, and the species Enterococcus lemanii and Enterococcus eurekensis, along with Acinetobacter towneri, a non-baumannii Acinetobacter that, while not typically pathogenic itself, is considered a public health threat because it can accumulate clinically relevant antimicrobial resistance genes potentially transferable to Acinetobacter baumannii, a notorious cause of hospital infections.

The findings sit within a broader and increasingly alarming literature on antimicrobial resistance spreading from livestock into the environment. Untreated poultry litter is a known reservoir of foodborne pathogens such as Campylobacter species, Listeria monocytogenes, Staphylococcus aureus, and Salmonella species, alongside antibiotic residues. In Cameroon, 100 percent of Escherichia coli and 36.4 percent of Salmonella isolates from chicken litter manure were found to be multidrug resistant, and some resistant bacteria carry plasmids that enable horizontal gene transfer, amplifying the spread of resistance genes. In South Africa, 56 percent of Enterococcus species isolated from agricultural soils following chicken litter application were resistant to at least one antibiotic, prompting calls to rethink manure use altogether. Enterococci, which dominated the Lagos farm soils, are notorious for developing resistance to critically important antibiotics.

Not everything in the altered microbiome is bad news. Lactobacillus species, the most abundant family in the farm soils, play a beneficial role in cycling nitrogen-containing compounds such as ammonia in poultry manure, potentially creating a safer environment for both birds and humans. Poultry litter is also a genuine organic fertilizer, supplying nitrogen, phosphorus, and potassium that boost crop growth and stimulate nitrifying bacteria. But the benefits come with well-documented environmental costs: excess phosphates from litter-amended fields can run off into water bodies and drive eutrophication, while nitrate leaching into groundwater has been reported in amended croplands. In neighboring Benin, documented cases of food poisoning from Campylobacter jejuni and Campylobacter coli were linked to leafy vegetables grown with poultry manure, illustrating how the practice can transmit pathogens directly into the food chain.

The Lagos team is careful about the limits of its work. The study covered only two farms and a single control site, a cross-sectional snapshot that may not capture the full dynamics of soil microbial change across larger scales or over time. Still, the researchers argue the data provide a crucial baseline for Nigeria, where livestock farming is economically vital but where, until now, there has been little molecular data on how poultry litter shapes soil microbiomes. Their conclusion is pragmatic rather than alarmist: poultry farming sustains income and nutrition for millions of households, so the answer is not to abandon litter as fertilizer but to treat it before it reaches the soil. The authors point to drying as a practical technology for reducing litter pollution, and they urge that untreated litter no longer be disposed of indiscriminately into pristine environments. As sequencing tools make it ever cheaper to read the microbial state of the ground beneath our feet, the message from Ikorodu is clear: what we spread on the land comes back to shape the invisible ecosystems that underpin soil health, food safety, and human health alike.

Subject of Research: The impact of poultry farming practices on soil bacterial community structure and composition in Lagos, Nigeria

Article Title: Contribution of poultry farm practice to the structure and composition of bacterial communities in the soil of poultry farms in Lagos, Nigeria

Article References: Contribution of poultry farm practice to the structure and composition of bacterial communities in the soil of poultry farms in Lagos, Nigeria. (n.d.). https://doi.org/10.1186/s44329-024-00015-1

Image Credits: AI Generated

DOI: 10.1186/s44329-024-00015-1

Keywords: poultry farming, soil microbiome, 16S rRNA sequencing, Firmicutes, Bacteroidetes, poultry litter, antimicrobial resistance, pathogenic bacteria, Nigeria, public health, metagenomics, soil health