Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility

Карначук, О. В.; Rusanov, Igor I; Panova, I. A.; Grigoriev, M. A.; Zyusman, Viacheslav S.; Latygolets, E. A.; Kadyrbaev, Maksat K.; Gruzdev, Eugeny V.; Beletsky, Alexey V.; Mardanov, Andrey V.; Pimenov, Nikolai V.; Ravin, Nikolai V.

doi:10.1038/s41598-021-90256-w

Cited by 22 publications

(18 citation statements)

References 51 publications

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“…Hydrogen sulfide production in swine manure slurry has been linked to Desulfovibrio spp. ( 12 ) and here genes encoding the dissimilatory sulfite reductase and involved in the metabolism of sulfate were only identified in the eight Desulfovibrionaceae MAGs. This included Desulfovibrio piger and Desulfovibrio sp900556755 as well as one MAG classified as Bilophila wadsworthia .…”

Section: Resultsmentioning

confidence: 89%

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

et al. 2022

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Section: Resultsmentioning

confidence: 89%

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

et al. 2022

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“…Hydrogen sulfide production in swine manure slurry has been linked to Desulfovibrio spp. (12) and here genes encoding the dissimilatory sulfite reductase and involved in the metabolism of sulfate were only identified in the eight Desulfovibrionaceae MAGs. This included Desulfovibrio piger and Desulfovibrio sp900556755 as well as one MAG classified as Bilophila wadsworthia .…”

Section: Resultsmentioning

confidence: 89%

Novel insights into the pig gut microbiome using metagenome-assembled genomes

Holman¹,

Kommadath²,

Tingley

et al. 2022

Preprint

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Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g. Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g. Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes.ImportanceMany of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The majority of these MAGs represented bacterial species that have yet to be cultured or described thus underlining the need for cultivation studies that isolate and describe novel bacterial species. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.

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“…Since the 16S rRNA gene profiling revealed the occurrence of SRB belonging to Desulfovibrionales and Desulfotomaculales in camel feces, the targeted isolation has been applied to members of these lineages. The initial SRB enrichment cultures were set up with a mixture of formate (7.5 mM) and acetate (2 mM) as an electron donor to prevent overgrowth with the abundant heterotrophic bacteria on the medium with organic acids [ 35 ]. The incubation temperature was 37 °C.…”

Section: Resultsmentioning

confidence: 99%

Active Sulfate-Reducing Bacterial Community in the Camel Gut

et al. 2023

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The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of −15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm−3 day−1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS2), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.

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Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility

Cited by 22 publications

References 51 publications

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

Novel insights into the pig gut microbiome using metagenome-assembled genomes

Active Sulfate-Reducing Bacterial Community in the Camel Gut

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