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Cited by 22Ruminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas ProductionGut microbiota and health

Reductive acetogenesis is a dominant process in the ruminant hindgut

Open access
Li, Qiushuang, Huo, Jiabin, Ni, Gaofeng, Zhang, Fan, Zhang, Shizhe, Zhang, Xiumin, Wang, Rong, Jiao, Jinzhen +9 more·2025·Microbiome
DOI 10.1186/s40168-024-02018-1PMC PMC11773752

Published version of a preprint

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Abstract

Abstract Background The microbes residing in ruminant gastrointestinal tracts convert plant biomass to nutritious volatile fatty acids, the primary energy source for ruminants. Ruminants´ gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), each with contrasting structures and functions in anaerobic digestion. With most previous studies focusing on the rumen microbiome, the cecal microbiome is much less investigated and understood, including the assembling microbial communities and overriding pathways of hydrogen metabolism. Results Here we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as experimental ruminant model. In situ measurements showed that acetate and hydrogen levels were both higher in the cecum than in the rumen. Concurrently, microbes capable of host mucin degradation and fermentative hydrogen production were more abundant in the cecum, whereas fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea were less abundant. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum, and genome-resolved analysis unveiled that cecum acetogens are both phylogenetically and functionally novel. Two in vitro experiments further supported that the pathways of hydrogen metabolism differ between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, a comparative analysis showed a strong enrichment of reductive acetogens in the hindguts of other ruminants. Conclusions These findings, by revealing an enrichment of acetogenesis in an important part of the gastrointestinal tract, reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts.

AI snapshot

Written from the paper’s full text.

TL;DR

The study comparatively profiled the rumen and cecum microbiomes of goats and found that reductive acetogenesis is enriched and active in the hindgut, with higher dissolved H2 and acetate in the cecum than in the rumen. Comparative metagenomic analysis across multiple ruminants further indicated that acetogens are consistently enriched in hindguts.

Key findings

  • Cecal digesta had four-fold higher dissolved H2 (p < 0.001), higher total VFAs (p < 0.01), higher acetate concentration and molar proportion (p < 0.001), but lower propionate (p < 0.01) and butyrate (p < 0.001) molar proportions than rumen digesta.
  • The cecum had 6.7-fold lower total bacteria (p < 0.01) and 2.8-fold lower methanogens (p < 0.01), but the methanogen-to-bacteria ratio was higher (3.1% vs 1.3%).
  • The reductive acetogenesis marker gene acsB was 12-fold more abundant in the cecum than in the rumen (p < 0.001), and nine Wood-Ljungdahl pathway genes were enriched in the cecum.
  • Across ruminants, cecal enrichment of acsB relative to rumen was 22-fold in dairy cows, 58-fold in goats, 111-fold in roe deer, 14-fold in sheep, ten-fold in water buffalo, 133-fold in water deer, and 20-fold in yak (p < 0.001).

Methods

  • Sixteen healthy goats (average body weight 19.1 ± 2.75 kg) were sampled before morning feeding; rumen and cecum digesta and epithelium were used for pH, dissolved H2, VFA, microbial DNA, and tissue RNA measurements.
  • Microbial profiling used 16S rRNA gene amplicon sequencing, qPCR, shotgun metagenomics, metagenomic binning (2358 nonredundant MAGs; 2324 bacterial, 34 methanogenic), CAZyme and hydrogenase/terminal reductase annotation, and genome-resolved phylogenetic analysis.
  • Two in vitro experiments compared rumen and cecal inocula: Experiment 1 used corn stover as substrate for 72 h, and Experiment 2 measured headspace H2 utilization and methane production over 48 h without added substrate; statistical tests included paired t-tests and Wilcoxon rank-sum tests with FDR adjustment.

Limitations

  • The paper does not state a dedicated limitations section.
  • The main in situ evidence comes from goats; extension to other ruminants relies on comparative metagenomic data from a previous study rather than direct in situ measurements in those species.
  • The authors note that acetogens from the hindgut still need to be isolated and their metabolic features investigated, and they caution that some glycoside hydrolase fold changes were numerically close to unity and would need enzyme activity verification.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1186/s40168-024-02018-1

Cites

90 of 90 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

7 of 16 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured

  • Findingcitation

    Linear discriminant analysis identified 15 key bacterial genera differentially abundant between the rumen and cecum.

    “Linear discriminant analysis (LDA) identified 15 key bacterial genera differentially abundance between the two gastrointestinal regions [29] (p < 0.001, Fig. 1M, Additional File S4).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [29] Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60. source
  • Findingown data

    Proteins involved in VFA absorption and intracellular pH regulation (HMGCS, HMGCL, ATPeV1B, BDH) were expressed at a higher level in the rumen than in the cecum.

    “proteins involved in VFA absorption and intracellular pH regulation, including 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS), 3-hydroxy-3-methylglutaryl-CoA lyase (HMGCL), vacuolar H+ ATPase subunit B (ATPeV1B), and β-hydroxybutyrate dehydrogenase (BDH) [26–28], were expressed at a higher level in the rumen than in the cecum (p < 0.001, Fig. 1I).”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [26] Yan L, Zhang B, Shen Z. Dietary modulation of the expression of genes involved in short-chain fatty acid absorption in the rumen epithelium is related to short-chain fatty acid concentration and pH in the rumen of goats. J Dairy Sci. 2014;97:5668–75. source
    • cites [27] Laarman AH, Ruiz-Sanchez AL, Sugino T, Guan LL, Oba M. Effects of feeding a calf starter on molecular adaptations in the ruminal epithelium and liver of Holstein dairy calves. J Dairy Sci. 2012;95:2585–94. source
    • cites [28] Xie F, Xu L, Wang Y, Mao S. Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep. MSystems. 2021;6:e00915–e921. source

      The Results section on epithelial gene expression identifies HMGCS1, HMGCL, and BDH1/BDH2 as VFA-metabolism or ketogenesis genes, but lists different genes for VFA absorption and intracellular pH regulation; it does not address ATPeV1B. The rumen-versus-cecum expression comparison is presented after the citation as the citing paper’s own Fig. 1I result, so it is not assessed as a finding attributed to this source. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    The increased acetate production and decreased methane production by the fiber-selected microbiome can be attributed to a greater community of reductive acetogens.

    “Inoculation with fiber-selected microbiome showed the paradoxically increased acetate production with decreased methane production than starch-selected microbiome, and could be attributed to the greater community of reductive acetogens [41].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [41] Li QS, Wang R, Ma ZY, Zhang XM, Jiao JZ, Zhang ZG, et al. Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants. ISME J. 2022;16:1–12. source
  • Premisecitation

    Acetate production through reductive acetogenesis is an H2 sink.

    “Acetate production during fermentative carbohydrate fermentation is accompanied by H2 release, whereas acetate production through reductive acetogenesis is an H2 sink [51].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [51] Ungerfeld EM. Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions. Front Microbiol. 2020;11:589. source
  • Findingown data

    Some CAZymes genes were more abundant in the rumen microbiome than in the cecum microbiome.

    “some CAZymes genes were more abundant in the rumen microbiome (p < 0.01, Additional Fig. S6)”
    Quote in the paperNot a substantial claim
  • May combine two claims. 35
  • Classified as probably not a substantial claim. 11
  • The quote only partly states this claim. 4

  • May combine two claims.

    Interpretationreasoning

    These findings suggest that the cecum favors reductive acetogenesis over hydrogenotrophic respiration, consistent with the higher concentration of dH2 in the cecum, which can enhance the competitiveness of reductive acetogenesis.

    “Altogether, these findings suggest that the cecum favors reductive acetogenesis over hydrogenotrophic respiration, consistent with the higher concentration of dH2 in the cecum (Fig. 1D), which can enhance the competitiveness of reductive acetogenesis [42, 43].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [42] Ungerfeld EM. A theoretical comparison between two ruminal electron sinks. Front Microbiol. 2013;4:319. source
    • cites [43] Ma ZY, Zhang XM, Wang M, Wang R, Jiang ZY, Tan ZL, et al. Molecular hydrogen produced by elemental magnesium inhibits rumen fermentation and enhances methanogenesis in dairy cows. J Dairy Sci. 2019;102:5566–76. source

  • Classified as probably not a substantial claim.

    Premisecitation

    Elevated fermentative acetate production is consistently associated with an increase in methane production.

    “Generally, elevated fermentative acetate production is consistently associated with an increase in methane production [52, 53].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [52] Wang M, Wang R, Xie TY, Janssen PH, Sun XZ, Beauchemin KA, et al. Shifts in Rumen fermentation and microbiota are associated with dissolved ruminal hydrogen concentrations in lactating dairy cows fed different types of carbohydrates. J Nutr. 2016;146:1714–21. source
    • cites [53] Beauchemin KA, Ungerfeld EM, Eckard RJ, Wang M. Review: Fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation. Animal. 2020;14:s2–16. source

      The “Rumen fermentation and microbiome associated with methanogenesis” section (page unavailable) explains that fermentation to volatile fatty acids releases hydrogen, much of which methanogens use to produce methane. It does not establish that elevated fermentative acetate production is consistently associated with increased methane production; it also distinguishes reductive acetate formation as an alternative hydrogen sink. (LLM, conf=0.78)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Acetate production during fermentative carbohydrate fermentation is accompanied by H2 release.

    “Acetate production during fermentative carbohydrate fermentation is accompanied by H2 release, whereas acetate production through reductive acetogenesis is an H2 sink [51].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [51] Ungerfeld EM. Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions. Front Microbiol. 2020;11:589. source

      The Background section on volatile fatty acid balances says acetate production from glucose releases metabolic hydrogen ([H]), but it does not establish that H2 is always released: it also identifies an acetate-producing pathway with no net [H] production. The Background section on other hydrogen-incorporating pathways explicitly describes reductive acetogenesis as using H2 to produce acetate, supporting the sentence’s second clause. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    The 2324 bacterial MAGs were distributed across 19 phyla, with Firmicutes (1463 MAGs), Bacteroidota (637 MAGs), and Spirochaetota (70 MAGs) being the most predominant.

    “The 2324 bacterial MAGs were distributed across 19 phyla, with Firmicutes (represented by 1463 MAGs), Bacteroidota (637 MAGs), and Spirochaetota (70 MAGs) being the most predominant (Fig. 3A, Additional File S9).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The rumen had a higher abundance of glycoside hydrolases degrading cellulose (3.80-fold higher) and hemicellulose (3.45-fold higher) than the cecum.

    “The rumen had a higher abundance GHs degrading cellulose (p < 0.001, 3.80-fold higher) and hemicellulose (p < 0.001, 3.45-fold higher)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The cecum had a slightly higher pH than the rumen.

    “Although the cecum had a slightly higher pH (p < 0.001, Fig. 1C)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    At the phylum level, Bacteroidota and Spirochaetota were enriched in the rumen, whereas Firmicutes, Verrucomicrobiota, Proteobacteria, and Actinobacteriota were relatively more abundant in the cecum.

    “At the phylum level, Bacteroidota and Spirochaetota were enriched in the rumen microbiota, whereas Firmicutes, Verrucomicrobiota, Proteobacteria, and Actinobacteriota were relatively more abundant in the cecum microbiota (p < 0.001, Fig. 1L, Additional File S3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The cecum was enriched with MAGs classified as Faecousia, Akkermansia, and Alistipes, and these MAGs encoded GH123, a GH enzyme involved in hydrolyzing host glycans.

    “Notably, the cecum was enriched with MAGs classified as Faecousia, Akkermansia, and Alistipes, and these MAGs encoded GH123, a GH enzyme involved in hydrolyzing host glycans (p < 0.05, Fig. 3B, Additional File S10).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Metagenomic binning yielded 2358 medium- or higher-quality metagenome-assembled genomes (MAGs, completeness ≥ 50% and contamination ≤ 10%) after quality control and dereplication.

    “we performed metagenomic binning, yielding 2358 medium- or higher-quality metagenome-assembled genomes (MAGs, completeness ≥ 50% and contamination ≤ 10%) after quality control and dereplication (Additional File S9).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The rumen was enriched in 17 glycoside hydrolases (e.g., GH2, GH10) and the cecum was enriched in 7 glycoside hydrolases (e.g., GH16, GH141) encoding hemicellulases.

    “the rumen enriched in 17 GHs (e.g., GH2, GH10) and the cecum enriched in 7 GHs (e.g., GH16, GH141)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing), S4 (based).

    Findingown data

    The rumen microbiome encoded a greater proportion of genes involved in sulfate reduction (adenylylsulfate reductase, aprA, 7.4-fold higher) than the cecum.

    “and sulfate reduction (adenylylsulfate reductase, aprA, p < 0.001, 7.4-folder higher)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The rumen displayed a greater abundance of sensory group C2 [FeFe]-hydrogenases (4.1-fold higher) and energy-converting 4e [NiFe]-hydrogenases (1.7-fold higher).

    “In contrast, the rumen displayed a greater abundance of sensory group C2 [FeFe]-hydrogenases (4.1-fold higher) and energy-converting 4e [NiFe]-hydrogenases (1.7-fold higher) (p < 0.001, Fig. 2C, Additional File S8).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The rumen-enriched MAGs were assigned to Prevotella, Cryptobacteroides, Ruminococcus, and Butyrivibrio, and they mainly encode cellulases (e.g., GH3) and hemicellulases (e.g., GH43).

    “In contrast, the rumen-enriched MAGs were assigned to Prevotella, Cryptobacteroides, Ruminococcus, and Butyrivibrio (p < 0.01), and they mainly encode cellulases (e.g., GH3) and hemicellulases (e.g., GH43) (Fig. 3B, Additional File S10).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Most bacterial MAGs encoded glycoside hydrolases, with 80% encoding enzymes involved in cellulose degradation, 81% in hemicellulose degradation, and 72% in host glycan degradation.

    “Most bacterial MAGs encoded GHs, with 80% encoding enzymes involved in the degradation of cellulose (80% MAGs), hemicellulose (81%), and host glycans (72%).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The most abundant family of CAZymes in both the rumen and cecum was glycoside hydrolases (GH).

    “The most abundant family of CAZymes in both regions were glycoside hydrolases (GH) (Additional File S5)”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    GPR43 protein expression is reduced in cecum papillae compared to the rumen.

    “Immunofluorescent staining revealed reduced levels of GPR43 in cecum papillae (Fig. 1G)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Ruminococcaceae UCG-005 and Christensenellaceae R7 were the most abundant and representative cecal genera.

    “Ruminococcaceae UCG-005 and Christensenellaceae R7 were the most abundant and representative cecal genera (Additional Fig. S4)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Halobacteriota MAGs were distributed in both regions but were enriched in the cecum.

    “while Halobacteriota MAGs were distributed in both regions, they were enriched in the cecum”
    Quote in the paperNot a substantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    Acetate levels positively correlated with Ruminococcaceae UCG-005, Christensenellaceae R7, and several other genera, with the strongest correlation with Akkermansia, Bacteroidales UCG_010_ge, Ruminococcaceae UCG_002, and unclassified Lachnospiraceae.

    “Acetate levels positively correlated with these two genera and several other genera, with the strongest correlation with Akkermansia, Bacteroidales UCG_010_ge, Ruminococcaceae UCG_002, and unclassified Lachnospiraceae (Additional Fig. S5).”
    Quote in the paperNot a substantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    The cecum had a higher concentration and molar proportion of acetate than the rumen.

    “In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The trimeric group A3 [FeFe]-hydrogenases were the most abundant in both gastrointestinal regions and were highly enriched in the cecum.

    “The trimeric group A3 [FeFe]-hydrogenases (identified based on the presence of genes encoding the bifurcating hydrogenase subunit hydA and diaphorase subunit hydB) were the most abundant in both gastrointestinal regions and were highly enriched in the cecum (Fig. 2C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Reductive acetogens were particularly abundant in the cecum of dairy cattle and buffalo, while water deer exhibited relatively lower abundance.

    “Notably, reductive acetogens were particularly abundant in the cecum of dairy cattle and buffalo, while water deer exhibited relatively lower abundance.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the rumen microbiome, the most enriched MAGs were Desulfovibrio and Succiniclasticum, capable of hydrogenotrophic sulfate and fumarate reduction, respectively.

    “In the rumen microbiome, the most enriched were Desulfovibrio and Succiniclasticum MAGs capable of hydrogenotrophic sulfate and fumarate reduction, respectively (p < 0.001, Fig. 3B, Additional File S11).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A greater number of acetogens were enriched in the cecum, where 15 MAGs (e.g., HGM12587 and SIG483) were enriched in the cecum and 9 others (e.g., SIG280 and RGIG7114) were enriched in the rumen.

    “with a greater number of acetogens enriched in the cecum, where 15 MAGs (e.g., HGM12587 and SIG483) enriched in the cecum and 9 others (e.g., SIG280 and RGIG7114) enriched in the rumen (Fig. 4A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The MAGs from each of the five novel genera encoded the complete set of enzymes of the Wood-Ljungdahl pathway, together with the group A3 [FeFe]-hydrogenase, Nfn transhydrogenase, and energy-converting Rnf or Ech enzymes.

    “This is further supported by detailed annotation, which shows that the MAGs from each of the five novel genera encoded the complete set of enzymes of the Wood-Ljungdahl pathway, together with the group A3 [FeFe]-hydrogenase, Nfn transhydrogenase, and energy-converting Rnf or Ech enzymes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the second in vitro experiment, both rumen and cecal microbiomes significantly decreased H2 levels compared to the uninoculated control and increased headspace methane concentration, approaching an asymptote.

    “Both rumen and cecal microbiomes significantly decreased H2 levels compared to the uninoculated control and increased headspace methane concentration, approaching an asymptote (p < 0.05, Fig. 5B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A total of 300 MAGs (13%) encoded both H2-consuming hydrogenases and terminal reductases, including those involved in reductive acetogenesis (52 MAGs), fumarate reduction (176 MAGs), nitrate ammonification (34 MAGs), and sulfate reduction (65 MAGs).

    “A total of 300 MAGs (13%) encoded both H2-consuming hydrogenases and terminal reductases, including those involved in reductive acetogenesis (52 MAGs), fumarate reduction (176 MAGs), nitrate ammonification (34 MAGs), and sulfate reduction (65 MAGs) (Additional File S11).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the first in vitro experiment with corn stover as substrate, rumen inocula demonstrated increased dry matter degradability, VFA concentrations, and methane production compared to cecum inocula.

    “In the first experiment, corn stover served as the substrate, the rumen inocula demonstrated increased dry matter degradability (DMD), VFA concentrations, and methane production, whereas the cecum inocula exhibited greater H2 accumulation (p < 0.05, Fig. 5A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum.

    “Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    These organisms encoded either one or two copies of the canonical acetyl-CoA synthase gene, suggesting their potential to mediate acetogenesis.

    “a phylogenetic tree based on the AcsB sequences revealed that these organisms encoded either one or two copies of the canonical acetyl-CoA synthase gene, suggesting their potential to mediate acetogenesis (Fig. 4B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Inoculation with fiber-selected microbiome resulted in increased acetate production and decreased methane production compared to starch-selected microbiome.

    “Inoculation with fiber-selected microbiome showed the paradoxically increased acetate production with decreased methane production than starch-selected microbiome, and could be attributed to the greater community of reductive acetogens [41].”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea.

    “Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    After 48 h of incubation, the rumen microbiota consumed more gaseous H2 and produced more methane than the cecum microbiome.

    “After 48 h of incubation, the rumen microbiota consumed more gaseous H2 and produced more methane than the cecum microbiome (p < 0.05, Fig. 5B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The acsB gene is significantly enriched in the cecal microbiomes of all examined ruminants relative to their rumen microbiome (p < 0.001), by 22-fold in dairy cows, 58-fold in goats, 111-fold in roe deer, 14-fold in sheep, ten-fold in water buffalo, 133-fold in water deer, and 20-fold in yak.

    “Our comparative analysis revealed a significant enrichment of the acsB gene a marker signature gene of the reductive acetogenesis pathway in the cecal microbiomes of all the ruminants relative to their rumen microbiome (p < 0.001): by 22-fold in dairy cows, 58-fold in goats, 111-fold in roe deer, 14-fold in sheep, ten-fold in water buffalo, 133-fold in water deer, and 20-fold in yak (Fig. 6A).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: acsB is a marker signature gene of the reductive acetogenesis pathway.

  • May combine two claims.

    Findingown data

    In in vitro incubations with corn stover, cecum inocula resulted in a higher molar proportion of acetate and a higher acetate-to-propionate ratio than rumen inocula.

    “Further analysis of the VFA profiles indicated that rumen inocula had a higher molar proportion of propionate whereas the cecum inocula resulted in a higher molar proportion of acetate with a concurrently increased acetate-to-propionate ratio (p < 0.05, Fig. 5A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    These findings suggest elevated H2 production and distinct H2 cycling processes in the cecum, which aligns with observed higher dH2 concentrations in the cecal samples.

    “Altogether, these findings suggest elevated H2 production and distinct H2 cycling processes in the cecum, which aligns with observed higher dH2 concentrations detected in the cecal samples (Fig. 1D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Increased dissolved hydrogen concentrations indicate distinct processes and reduced coupling between fermentative H2 production and utilization in the cecum.

    “Such significantly increased dH2 concentrations indicate distinct processes and reduced coupling between fermentative H2 production and utilization in the cecum.”
    • Also stated in: § Results · hedged
      “Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Ruminants rely on mutualistic microbes in their digestive system to convert plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants.

    “These microbes enable ruminants to derive most of their energy and nutrients from otherwise indigestible fibrous plant cell wall materials [2, 3].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [2] Pérez-Barbería FJ. The Ruminant: Life History and Digestive Physiology of a Symbiotic Animal. In: García-Yuste S, editor. Sustainable and Environmentally Friendly Dairy Farms. Cham: Springer International Publishing; 2020:19–45. source
    • cites [3] Mizrahi I, Wallace RJ, Moraïs S. The rumen microbiome: balancing food security and environmental impacts. Nat Rev Microbiol. 2021;19:553–66. source

  • May combine two claims.

    Interpretationown data

    VFA absorption through cecal papillae is probably slower than through rumen papillae, explaining the relatively higher VFA concentration in the cecum at least in part.

    “These results indicate that VFA absorption through cecal papillae is probably slower than that through the rumen papillae, explaining the relatively higher VFA concentration in the cecum, at least in part.”
    • Also stated in: § Results · hedged
      “higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    MAGs with a completeness of at least 50% and a contamination rate of at most 10% were retained and dereplicated at a 99% average nucleotide identity cutoff.

    “The MAGs with a completeness of ≥ 50% and a contamination rate of ≤ 10% (3439 MAGs) were then dereplicated using dRep [67] (version 3.3.0) at a 99% average nucleotide identity (ANI) cutoff.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Interpretationown data

    Acetogenesis is enriched in the cecum, a key region of the gastrointestinal tract.

    “These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    All p values were adjusted for FDR using the Benjamini-Hochberg method.

    “All p values were adjusted for FDR using the Benjamini–Hochberg method.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    These results point to distinct microbes selected in the rumen and the cecum that utilize different pathways of H2 metabolism, with acetogenesis likely being a significant H2 sink within the cecal microbiome.

    “These results point to distinct microbes selected in the rumen and the cecum that utilize different pathways of H2 metabolism, with acetogenesis likely being a significant H2 sink within the cecal microbiome.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    These findings indicate that the rumen microbiome possesses a greater capacity for fiber degradation and hydrogenotrophic methanogenesis, leading to lower H2 accumulation.

    “These findings indicate that the rumen microbiome possesses a greater capacity for fiber degradation and hydrogenotrophic methanogenesis, leading to lower H2 accumulation.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    For CAZymes annotation, a query was accepted only if all three approaches (DIAMOND, dbCAN_sub, and dbCAN) reported the same match.

    “A query was acceptable only if all three approaches (DIAMOND, dbCAN_sub, and dbCAN), reported the same match.”
    Quote in the paperNot a substantial claim
45 of 45

  • The paper relies on this without support.

    The cecal microbiome remains much less investigated and understood than the rumen microbiome, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

    “While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.”

  • The paper relies on this without support.

    We currently lack a detailed species-resolved understanding of the processes and mediators controlling nutrient cycling between the rumen and the cecum.

    “However, we currently lack a detailed species-resolved understanding of the processes and mediators controlling nutrient cycling between the two regions.”

  • The paper relies on this without support.

    Most enteric methane produced in ruminants originates in the rumen rather than the hindgut.

    “It is well-konwn that most of the enteric methane produced in ruminants originates in the rumen rather than the hindgut”

  • The paper relies on this without support.

    Differences in the morphological and nutrient composition of the rumen and cecum select for compositionally and functionally distinct microbiota.

    “Differences in the morphological and nutrient composition of rumen and cecum likely select for compositionally and functionally distinct microbiota.”

  • The paper relies on this without support.

    acsB is a marker signature gene of the reductive acetogenesis pathway.

    “the acsB gene a marker signature gene of the reductive acetogenesis pathway”

  • The paper relies on this without support.

    A high abundance of genes encoding key enzymes of the Wood-Ljungdahl pathway indicates enrichment of reductive acetogenesis.

    “The enrichment of reductive acetogenesis in the cecal microbiome was further supported by a high abundance of other genes encoding key enzymes involved in the Wood-Ljungdahl pathway (Additional File S13).”

  • The paper relies on this without support.

    The rumen and cecum are the two primary fermentation sites of ruminants.

    “the two primary fermentation sites of ruminants”
7 of 7

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Conflicting incubation times for the first experiment's VFA samples

    Minor

    Figure 5 describes VFA profiles from the corn-stover experiment after 72 hours, but the methods say liquid samples from the in vitro experiments were collected after 48 hours. The stated collection time for those VFA samples is therefore inconsistent.

1 of 1

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Authors
Li, Q., Huo, J., Ni, G., Zhang, F., Zhang, S., Zhang, X., Wang, R., Jiao, J., Yu, Z., Pu, X., Yue, Y., Ungerfeld, E. M., Zhang, X., Wu, J., Tan, Z., Greening, C., & Wang, M.
Affiliations
  • Chinese Academy of Sciences (CN)
  • Monash University (AU)
  • The Ohio State University (US)
  • Instituto de Investigaciones Agropecuarias (CL)
Corresponding author
Wang, Min
ORCID
Venue
Microbiome
Publisher
Springer Science and Business Media LLC
Published
2025-01-28
Volume
13
Issue
1
Pages
28-28
ISSN
2049-2618 (ISSN-L)
DOI
10.1186/s40168-024-02018-1
PMC
PMC11773752
OpenAlex
W4406886564
Semantic Scholar
bb9736044ba78c51245bf428142c9f2f007ff37a
Cited by
22
References
89
Citations by year
2026: 11 · 2025: 9 · 2024: 2
FWCI
20.07
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbiome (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (U22A20512, APP1178715)
  • National Health and Medical Research Council (1178715)
  • National Key Research and Development Program of China (2023YFD1300902)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
  • Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
reductive acetogenesis, cecal microbiota, rumen microbiome, hydrogen metabolism, volatile fatty acids, acetate production, methanogenesis, mucin-degrading bacteria, hydrogenotrophic bacteria, goats, genome-resolved metagenomics
MeSH terms
Gastrointestinal Microbiome, Acetates, Animals, Archaea, Bacteria, Cecum, Fatty Acids, Volatile, Fermentation, Goats, Hydrogen, Methane, Rumen, Ruminants

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

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