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Cited by 50Ruminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas ProductionGut microbiota and health

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production

Open access
Mi, Lan, Yang, Bin, Hu, Xialu, Luo, Yang, Liu, Jianxin, Yu, Zhongtang, Wang, Jiakun·2018·Frontiers in Microbiology
DOI 10.3389/fmicb.2018.00575PMC PMC5890152
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Abstract

The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber. pH in the sheep rumen was more than 1 unit higher than that in the rabbit cecum. The acetate to propionate ratio in the rabbit cecum was more than 3-fold greater than that in the sheep rumen. Comparative analysis of 16S rRNA gene amplicon libraries revealed distinct microbiota between the rumen of sheep and the cecum of rabbits. Hydrogen-producing fibrolytic bacteria, especially Butyrivibrio, Succiniclastium, Mogibacterium, Prevotella, and Christensenellaceae, were more predominant in the sheep rumen, whereas non-hydrogen producing fibrolytic bacteria, such as Bacteroides, were more predominant in the rabbit cecum. The rabbit cecum had a greater predominance of acetogens, such as those in the genus Blautia, order Clostridiales, and family Ruminococcaceae. The differences in the occurrence of hydrogen-metabolizing bacteria probably explain much of the differential methane outputs from the rumen and the cecum. Future research using metatranscriptomics and metabolomics shall help confirm this premise and understand the factors that shape the differential microbiota between the two digestive organs. Furthermore, our present study strongly suggests the presence of new fibrolytic bacteria in the rabbit cecum, which may explain the stronger fibrolytic activities therein.

AI snapshot

Written from the paper’s full text.

TL;DR

Sheep rumen and rabbit cecum differ in fermentation environment and microbiota, and these differences help explain why sheep produce much more methane than rabbits on the same alfalfa hay diet. The rabbit cecum appears to rely more on acetogenesis and harbors greater fibrolytic enzyme activity, while the sheep rumen has more hydrogen-producing microbes and methanogens.

Key findings

  • Sheep emitted substantially more CH4 than rabbits per unit BW0.75, DMI, digestible NDF, and digestible ADF; the sheep CH4:CO2 ratio was 6.4 times higher, and rabbits produced no more than ¼ of the sheep CH4 output on those bases.
  • Rumen pH was 7.11 ± 0.17 versus cecal pH 5.82 ± 0.25, and the cecal acetate:propionate ratio was 19.34 ± 1.07 versus 5.70 ± 0.50 in the rumen.
  • Hydrogen-producing fibrolytic bacteria such as Butyrivibrio, Succiniclasticum, Mogibacterium, Prevotella, and Christensenellaceae were more predominant in the sheep rumen, whereas Bacteroides and acetogen-associated taxa such as Blautia, Clostridiales, and Ruminococcaceae were more predominant in the rabbit cecum.
  • The rabbit cecum had higher MCP (30.76 ± 2.03 vs. 24.01 ± 2.78 mg/g), CMCase (4.20 ± 0.48 vs. 2.00 ± 0.30 U/g), MCCase (5.86 ± 0.43 vs. 2.06 ± 0.16 U/g), and pectinase (20.40 ± 3.29 vs. 8.80 ± 1.15 U/g) activities, while xylanase activity was similar.

Methods

  • Five adult male sheep (63.91 ± 6.18 kg BW) and fifteen adult male New Zealand White rabbits (3.14 ± 0.14 kg BW) were fed the same alfalfa hay diet; gas production was measured in open-circuit respiratory chambers, and rumen or cecal contents were collected for fermentation and microbial analyses.
  • The study measured feed intake and digestibility, CH4 and CO2 yields, VFA concentrations, microbial crude protein, fibrolytic enzyme activities, and microbial abundances by real-time PCR.
  • Archaeal and bacterial microbiota were profiled by 16S rRNA gene amplicon sequencing on Illumina MiSeq, analyzed with QIIME and Greengenes, compared using weighted UniFrac/PCoA, and related to animal phenotypes using Pearson correlations and one-way ANOVA.

Limitations

  • The paper states that future metatranscriptomics and metabolomics are needed to confirm the premise and understand factors shaping the differential microbiota; it also states that Eh was not analyzed in the present study.
  • Evident from the design: the comparison confounds host species with digestive organ (sheep rumen vs. rabbit cecum), so organ-specific effects cannot be separated from species effects.
  • Evident from the text: sample sizes are small (n = 5 sheep; 15 rabbits, with microbiota analyses using 5 rabbit blocks), only one diet (alfalfa hay) was tested, and the microbial–methane relationships are correlational rather than causal.

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

Integrity signals

Registry

Crossref · 10.3389/fmicb.2018.00575

Cites

63 of 63 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

15 of 40 cited sources checked · 6 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Methanogenesis is inhibited at low pH, as exemplified by no CH4 production at pH 5.5 or below in in-vitro cultures inoculated with rumen fluid from roughage-fed cows.

    “It is well documented that methanogenesis is inhibited at low pH, as exemplified by no CH4 production at pH 5.5 or below in in-vitro cultures inoculated with rumen fluid from roughage-fed cows (Russell, 1998).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Russell, 1998 source

      The Results and Discussion report that low pH reduced CH4 production in vitro, including incubations using bacteria from forage-fed cows. The paper reports a more-than-twofold decline in CH4 production below pH 5.7, but the text does not establish the claimed absence of CH4 production at pH 5.5 or below. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    Several studies revealed a strong correlation between CH4 yields and archaea:bacteria ratio.

    “Several studies revealed a strong correlation between CH4 yields and archaea: bacteria ratio (Wallace et al., 2014), and a similar finding was found in the present study.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wallace et al., 2014 source

      The Results report a correlation between methane emissions and the archaea:bacteria ratio, and the Discussion calls it strong within the high-concentrate diet. The paper reports no significant correlation for the medium-concentrate diet. It is one study of methane emissions in beef steers, not evidence that several studies found a strong correlation with CH4 yield. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Premisecitation

    Among the bacterial genera whose relative abundance was strongly and positively correlated with CH4 yield, Prevotella and related bacteria, Butyrivibrio, and Succiniclasticum are unique and/or predominant hydrogen-producing bacteria in the rumen.

    “Among the bacterial genera whose relative abundance was strongly and positively correlated with CH4 yield, Prevotella and related bacteria, Butyrivibrio, and Succiniclasticum are unique and/or predominant hydrogen-producing bacteria in the rumen (Leahy et al., 2013).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Leahy et al., 2013 source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
  • Premisecitation

    The rumen Eh ranges from -268 to -318 mV.

    “Second, the Eh in the rabbit cecum ranges from -160 to -210 mV (Kimsé et al., 2010; Michelland et al., 2010), while the rumen Eh ranges from -268 to -318 mV (Mathieu et al., 1996).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Mathieu et al., 1996 source

      The Results section says rumen redox potential changed after feeding and with protozoa or probiotics, but the passages available from our copy do not give a range of −268 to −318 mV. Searches for those values and for Table IV’s redox-potential measurements did not locate the claimed endpoints. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Findingcitation

    A strong positive correlation was found between A:P ratio and some bacterial taxa, including some taxa of Clostridiales, Lachnospiraceae, Ruminococcaceae, and Blautia, all of which contain known acetogens.

    “A strong positive correlation was also found between A: P ratio and some bacterial taxa, including some taxa of Clostridiales, Lachnospiraceae, Ruminococcaceae, and Blautia, all of which contain known acetogens (Yang et al., 2016).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Yang et al., 2016 source

      The Results and Discussion sections on cecal environment and acetogen phylogeny report the A:P ratio and identify potential acetogen sequences affiliated with Lachnospiraceae, Ruminococcaceae, Blautia, and Clostridiaceae (page numbers unavailable). They do not report a strong positive correlation between the ratio and those taxa; the paper instead analyzes the ratio and taxa separately. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 14
  • May combine two claims. 34
  • The quote only partly states this claim. 1

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

    Premisecitation

    CH4 output is positively associated with bacterial populations that ferment ingested feed to relatively more hydrogen in sheep.

    “CH4 output was found to be positively associated with bacterial populations that ferment ingested feed to relatively more hydrogen in sheep (Kittelmann et al., 2014).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Kittelmann et al., 2014 source

  • Classified as probably not a substantial claim.

    Premisecitation

    Species of Blautia including B. coccoides, B. hydrogenotrophica, and B. schinikii, known acetogens, were found at high predominance in rabbit cecum.

    “In a recent study, species of Blautia including B. coccoides, B. hydrogenotrophica, and B. schinikii, which are known acetogens, were found at high predominance in rabbit cecum (Yang et al., 2016).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Yang et al., 2016 source

      The General Discussion says that a dominant rabbit-cecal acetogen was affiliated with Blautia and identifies B. coccoides, B. hydrogenotrophica, and B. schinkii as known acetogens. It does not say those three species themselves were found at high predominance; the phylogenetic analysis says most detected OTUs could not be classified to species or genus. The citing sentence also spells B. schinkii as “B. schinikii.” (LLM, conf=0.88)

      Experimental — accuracy not yet measured

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

    Premisecitation

    The genus Methanobrevibacter is the most ubiquitous and predominant hydrogenotrophic methanogen in the foregut and hindgut of herbivores.

    “The genus Methanobrevibacter is the most ubiquitous and predominant hydrogenotrophic methanogens found in the foregut and hindgut of herbivores (Kušar and Avguštin, 2010; St-Pierre and Wright, 2013) although several species of Methanomassiliicoccales can use methyl substrates (Poulsen et al., 2013).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites Kušar and Avguštin, 2010 source
    • cites St-Pierre and Wright, 2013 source
    • cites Poulsen et al., 2013 source

      Poulsen et al. is attached to the sentence’s methyl-substrate clause, not to the preceding claim about Methanobrevibacter. The section “Methylotrophic methanogenesis from methylamines (MAs)” reports methylamine use by rumen-cluster Thermoplasmata and methanol use by the related Methanomassiliicoccus luminyensis. It does not establish that several identified species can use methyl substrates. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Methanogenesis in the rumen and hindgut is predominantly driven via the hydrogenotrophic pathway using H2 and CO2 (also formate) as substrates.

    “Methanogenesis in the rumen and hindgut is predominately driven via the hydrogenotrophic pathway using hydrogen (H2) and CO2 (also formate) as the substrates (Liu and Whitman, 2008) though some CH4 is also produced through the methylotrophic methanogenesis pathway using methanol and methylamines as the substrates (Poulsen et al., 2013).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Liu and Whitman, 2008 source
    • cites Poulsen et al., 2013 source

  • May combine two claims.

    Premisecitation

    In the rumens of high methane-emitting sheep, members of Ruminococcaceae and Lachnospiraceae were found at higher relative abundance, while the rumens of low methane-emitting sheep were enriched with Erysipelotrichaceae, especially Sharpea spp.

    “In the rumens of high methane-emitting sheep, members of Ruminococcaceae and Lachnospiraceae were found at higher relative abundance, while the rumens of low methane-emitting sheep were enriched with Erysipelotrichaceae, especially Sharpea spp. (Kamke et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Kamke et al., 2016 source

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

    Premisecitation

    The previous study indicated that it was gene expression rather than gene abundance of methanogens that was strongly correlated with CH4 yields from sheep.

    “However, the previous study indicated that it was gene expression rather than gene abundance of methanogens that was strongly correlated with CH4 yields from sheep (Shi et al., 2014).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Shi et al., 2014 source

  • May combine two claims.

    Premisecitation

    Hydrogen-producing microbes provide the reducing power for hydrogenotrophic methanogenesis, and sheep producing more hydrogen also produced more CH4 than those that produced less hydrogen.

    “Hydrogen-producing microbes provide the reducing power for hydrogenotrophic methanogenesis, and indeed, sheep producing more hydrogen also produced more CH4 than those that produced less hydrogen (Kittelmann et al., 2014).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Kittelmann et al., 2014 source

      The Introduction states that rumen microbes produce H2 and methanogenic archaea use it to produce CH4. The Abstract and Discussion link higher CH4 yields in sheep to bacterial communities thought to produce more H2, but describe the difference in H2 production as a hypothesis, not a measured result for individual sheep. Page numbers were not supplied in our copy. (LLM, conf=0.87)

      Experimental — accuracy not yet measured

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

    Premisecitation

    It has been suggested that pH might determine the predominance of hydrogen disposal pathways, with relatively neutral pH favoring methanogens and acidic pH favoring acetogens.

    “It has been suggested that pH might determine the predominance of hydrogen disposal pathways, with relatively neutral pH favoring methanogens and acidic pH favoring acetogens (Gibson et al., 1990).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Gibson et al., 1990 source

  • May combine two claims.

    Premisecitation

    The rumen receives a large volume of saliva (about 1.31 L of saliva is secreted from one parotid gland per day for an adult sheep), which buffers the acidity from VFA.

    “The rumen receives a large volume of saliva (about 1.31 L of saliva is secreted from one parotid gland per day for an adult sheep), which buffers the acidity from VFA (McDougall, 1948), while cecum receives no saliva.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites McDougall, 1948 source

      The Results report an average of 1,310 mL per 24 hours from one parotid gland, and the discussion of saliva’s function (p. 104) describes its bicarbonate and phosphate as buffers for acids produced in the rumen. However, the reported average includes a six-month-old lamb, so it is not specifically an average for adult sheep. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Sheep emitted more CH4 than rabbits per unit of metabolic body weight, dry matter intake, digestible NDF, and digestible ADF.

    “The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber.”
    • Also stated in: § Feed Digestibility and Gas Yields · plain
      “Each of the sheep emitted substantially more CH4 than each rabbit per day per unit of BW0.75, DMI, digestible NDF, or digestible ADF (Figures 1A–D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    MCCase activity was higher in the rabbit cecum than in the sheep rumen per g content and per mg MCP.

    “A higher (P < 0.01) activity of CMCase, MCCase, and pectinase was observed in the rabbit cecum than in the sheep rumen either per g content or mg MCP.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The abundance of Ruminococcus albus, R. flavefaciens, Fibrobacter succinogenes, and Butyrivibrio fibrisolvens was greater in the sheep rumen than in the rabbit cecum.

    “The abundance of Ruminococcus albus, R. flavefaciens, Fibrobacter succinogenes, and Butyrivibrio fibrisolvens was greater in the sheep rumen than in the rabbit cecum.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Almost all bacterial sequences from both the sheep rumen and the rabbit cecum were assigned to known bacterial phyla, with Firmicutes (48.7 vs. 56.1%) and Bacteroidetes (47.4 vs. 36.1%) being represented by more sequences than other phyla.

    “Almost all the sequences obtained from both the sheep rumen and the rabbit cecum were assigned to known bacterial phyla, with Firmicutes (48.7 vs. 56.1%) and Bacteroidetes (47.4 vs. 36.1%) being represented by more sequences than other phyla (Figure 5A).”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    The rabbit cecum had a greater predominance of acetogens, such as those in the genus Blautia, order Clostridiales, and family Ruminococcaceae, than the sheep rumen.

    “The rabbit cecum had a greater predominance of acetogens, such as those in the genus Blautia, order Clostridiales, and family Ruminococcaceae.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Sheep had a higher apparent digestibility of DM, NDF, and ADF than rabbits.

    “However, the sheep had a higher apparent digestibility of DM, NDF, and ADF than the rabbits (P < 0.05).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The two digestive organs differed in molar proportions of VFA, with the rabbit cecum having higher acetate and butyrate but lower propionate than the sheep rumen.

    “The two digestive organs also differed (P ≤ 0.01) in molar proportions of VFA, with the rabbit cecum having a higher value for acetate and butyrate but a lower value for propionate.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The rabbit cecum had a lower archaeal Shannon diversity index and Simpson index of diversity than the sheep rumen.

    “The Chao1 richness estimate was similar between the two digestive organs, but the rabbit cecum had a lower Shannon diversity index and Simpson index of diversity than the sheep rumen (Table 4A).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Pectinase activity was higher in the rabbit cecum than in the sheep rumen per g content and per mg MCP.

    “A higher (P < 0.01) activity of CMCase, MCCase, and pectinase was observed in the rabbit cecum than in the sheep rumen either per g content or mg MCP.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    CMCase activity was higher in the rabbit cecum than in the sheep rumen per g content and per mg MCP.

    “A higher (P < 0.01) activity of CMCase, MCCase, and pectinase was observed in the rabbit cecum than in the sheep rumen either per g content or mg MCP.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A significant portion of archaeal sequences was assigned to known species: 36.3% to M. thaueri, 14.6% to M. woesei, and 10.8% to M. millerae for sheep rumen; 74.6% to M. woesei and 13.9% to M. thaueri for rabbit cecum.

    “A significant portion of the archaeal sequences was assigned to known species, with 36.3% assigned to ∗∗∗M. thaueri, 14.6% to M. woesei, and 10.8% to M. millerae for the sheep rumen sequences, while for the rabbit cecal sequences, 74.6% to M. woesei, and 13.9% to M. thaueri.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The number of OTUs, Chao1 richness estimate, Shannon diversity index, and Simpson index of diversity in the sheep rumen were all significantly greater than those in the rabbit cecum for bacteria.

    “The number of OTUs, Chao1 richness estimate, Shannon diversity index, and Simpson index of diversity in the sheep rumen were all significantly greater than those in the rabbit cecum (Table 4B).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    More than 95% of archaeal sequences from the rabbit cecum were assigned to the genus Methanobrevibacter, while sheep rumen archaeal sequences were assigned to Methanobrevibacter (68.3%), Methanosphaera (17.3%), and unidentified archaeon vadinCA11 (14.2%).

    “More than 95% of the archaeal sequences from the rabbit cecum were assigned to the genus Methanobrevibacter, while the archaeal sequences from the sheep rumen were assigned to Methanobrevibacter (68.3%), Methanosphaera (17.3%), and unidentified achaeon vadinCA11 (14.2%).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Ruminococcaceae, Clostridiales, Oscillospira, Blautia, and Clostridium were less predominant in the sheep rumen than in the rabbit cecum, while Christensenellaceae and candidate family S24-7 were more predominant in the sheep rumen than in the rabbit cecum.

    “A small number of taxa had different relative abundance between the sheep rumen and the rabbit cecum, with Ruminococcaceae (10.1 vs. 24.1%, P < 0.01), Clostridiales (12 vs. 18%, P = 0.03), Oscillospira (0.1 vs.1.2%, P < 0.01), Blautia (0.4 vs. 1.7%, P = 0.01), and Clostridium (0.5 vs. 1.7%, P = 0.01) being less predominant, while Christensenellaceae (2.2 vs. 0.1%, P < 0.01) and candidate family S2”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    M. ruminantium was found in both the digestive organs at low relative abundance and low correlation with CH4 yield.

    “M. ruminantium, one of the two species (M. ruminantium and M. Olleyae) in the Methanobrevibacter RO clade (Janssen and Kirs, 2008; Kittelmann et al., 2013), was found in both the digestive organs at low relative abundance and low correlation with CH4 yield.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Janssen and Kirs, 2008; Kittelmann et al., 2013

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingown data

    In total, 840 and 728 OTUs were observed in the sheep rumen and the rabbit cecum, respectively, and only 51 OTUs were found in both digestive organs.

    “In total, 840 and 728 OTUs were respectively observed in the sheep rumen and the rabbit cecum, and only 51 OTUs were found in both digestive organs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    As determined by qPCR, the sheep rumen had a greater abundance of R. albus, R. flavefaciens, B. fibrisolvens, fungi, and protozoa, all of which can produce hydrogen during feed fermentation, than the rabbit cecum.

    “As determined by qPCR, the sheep rumen did have a greater abundance of R. albus, R. flavefaciens, B. fibrisolvens, fungi, and protozoa, all of which can produce hydrogen during feed fermentation, than the rabbit cecum.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    The two digestive organs each harbored a distinct archaeal microbiota, with M. woesei being the dominant species in the rabbit cecum, whereas the sheep rumen contained M. thaueri as the most predominant known species followed by M. millerae and M. woesei.

    “The two digestive organs each harbored a distinct archaeal microbiota, with M. woesei being the dominant species in the rabbit cecum, whereas the sheep rumen containing M. thaueri as the most predominant known species followed by M. millerae and M. woesei.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The relative abundance of M. thaueri appeared to be positively correlated (P < 0.05) with Succiniclasticum, Mogibacterium, candidate family [Mogibacteriaceae], Prevotella, and CH4 yields, and was negatively (P < 0.05) correlated with Akkermansia.

    “The relative abundance of M. thaueri appeared to be positively correlated (P < 0.05) with Succiniclasticum, Mogibacterium, candidate family [Mogibacteriaceae], Prevotella, and CH4 yields, and was negatively (P < 0.05) correlated with Akkermansia.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The rabbit cecum had a lower abundance of RCC methanogens, non-RCC methanogens, and total methanogens (as quantified as mcrA gene copies/g sample) than the sheep rumen.

    “The rabbit cecum had a lower abundance of RCC methanogens, non-RCC methanogens, and total methanogens (as quantified as mcrA gene copies/g sample) than the sheep rumen.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The present study strongly suggests the presence of new fibrolytic bacteria in the rabbit cecum, which may explain the stronger fibrolytic activities therein.

    “Furthermore, our present study strongly suggests the presence of new fibrolytic bacteria in the rabbit cecum, which may explain the stronger fibrolytic activities therein.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Ruminants produce more CH4 than monogastric animals per unit of metabolic body weight or product.

    “Ruminants are the main producing animals of meat and milk, but they also produce more CH4 than monogastric animals per unit of BW0.75 or product (Franz et al., 2010).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Franz et al., 2010

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Premisecitation

    In the foregut of kangaroos, acetogens outcompete methanogens for CO2 and H2 and can synthesize acetate via the acetyl-CoA pathway, providing a significant energetic benefit to the host.

    “but in the foregut (tubular) of kangaroos, acetogens outcompete methanogens for CO2 and H2 and can synthesize acetate via the acetyl-CoA pathway, providing a significant energetic benefit to the host animal (Attwood and McSweeney, 2008).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Attwood and McSweeney, 2008 source

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

    Premisecitation

    Kangaroos, a group of tubiform foregut fermenters, have high passage rate and low CH4 production.

    “This premise is consistent with the high passage rate and low CH4 production by kangaroos, a group of tubiform foregut fermenters (Von Engelhardt et al., 1978).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Von Engelhardt et al., 1978 source

  • May combine two claims.

    Premisecitation

    The bacterial genera whose relative abundance appeared to be negatively correlated with CH4 yield are either acetogens (e.g., Blautia), butyrate producers (e.g., Oscillospira), or succinate producers (e.g., Bacteroides).

    “The bacterial genera whose relative abundance appeared to be negatively correlated with CH4 yield are either acetogens (e.g., Blautia) (Müller and Frerichs, 2013), butyrate producers (e.g., Oscillospira) (Gophna et al., 2017), or succinate producers (e.g., Bacteroides) (Song et al., 2015).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Müller and Frerichs, 2013; Gophna et al., 2017; Song et al., 2015

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Premisecitation

    Only one study has analyzed the archaeal microbiota in the cecum of rabbits, and M. woesei was represented by more cloned 16S rRNA gene sequences than other species.

    “Based on a literature search of the Pubmed, only one study has analyzed the archaeal microbiota in the cecum of rabbits, and M. woesei was represented by more cloned 16S rRNA gene sequences than other species (Kušar and Avguštin, 2010).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Kušar and Avguštin, 2010 source

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

    Interpretationnone given

    The tubiform and small diameter of the rabbit cecum may explain its relatively higher Eh.

    “The tubiform and small in diameter of the rabbit cecum may explain its relatively higher Eh.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The cecum is a tubiform tract, while the rumen is a large sac.

  • May combine two claims.

    Interpretationreasoning

    The structural difference between the tubiform cecum and the large sac rumen can cause a faster digesta passage rate through the rabbit cecum than through the sheep rumen, contributing to the less CH4 output from the rabbits than from the sheep.

    “Such structural difference can causes a faster digesta passage rate through the rabbit cecum than through the sheep rumen, contributing to the less CH4 output from the rabbits than from the sheep.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The cecum is a tubiform tract, while the rumen is a large sac.

  • May combine two claims.

    Premisecitation

    Methane is produced by methanogens, but other members of the microbiota can determine or profoundly affect the rate and yield of methanogenesis.

    “Methane is produced by methanogens, but other members of the microbiota can determine or profoundly affects the rate and yield of methanogenesis (Kittelmann et al., 2014; Danielsson, 2016).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Kittelmann et al., 2014; Danielsson, 2016

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    Both ruminants and non-ruminant herbivores emit CH4, but ruminants emit much more CH4 than non-ruminants.

    “Both ruminants and non-ruminant herbivores emit CH4, but the former emits much more CH4 than the latter (Franz et al., 2010, 2011; Cabezas Garcia, 2017).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Franz et al., 2010, 2011; Cabezas Garcia, 2017

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationown data

    The cecum of rabbits is potentially a rich resource to fibrolytic bacteria and hence novel cellulolytic enzymes.

    “The cecum of rabbits is potentially a rich resource to fibrolytic bacteria and hence novel cellulolytic enzymes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    The relatively lower pH in the cecum of rabbits probably suppresses hydrogenotrophic methanogenesis, allowing homoacetogenesis to increase.

    “The relatively lower pH in the cecum of rabbits probably suppress hydrogenotrophic methanogenesis, allowing homocaetogenesis to increase.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    The dominance of homoacetogenesis has been reported in some tubiform gut ecosystems, such as rabbits cecum, kangaroos foregut, and termite hindgut.

    “The dominance of homoacetogenesis has been reported in some tubiform gut ecosystems, such as rabbits cecum (Yang et al., 2016), kangaroos foregut (Gagen et al., 2010), and termite hindgut (Ottesen and Leadbetter, 2011).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Yang et al., 2016; Gagen et al., 2010; Ottesen and Leadbetter, 2011

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationreasoning

    Along with the significantly different bacterial microbiota structures between the sheep rumen and the rabbit cecum, the findings indicate that rabbit cecum probably harbors novel and uncharacterized cellulolytic bacteria and glycoside hydrolases.

    “Along with the significantly different bacterial microbiota structures between the sheep rumen and the rabbit cecum, our findings indicate that rabbit cecum probably harbors novel and uncharacterized cellulolytic bacteria and glycoside hydrolases.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Different microbiota were also reported between the rumen and the cecum of growing bulls, reindeer, and Chinese roe deer.

    “Different microbiota were also reported between the rumen and the cecum of growing bulls (Popova et al., 2017), reindeer (Wedlock et al., 2013), and Chinese roe deer (Li et al., 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Popova et al., 2017; Wedlock et al., 2013; Li et al., 2014

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Interpretationreasoning

    The lower pH in the rabbit cecum could also decrease the CO2 solubility and thus more CO2 emission.

    “The lower pH in the rabbit cecum could also decrease the CO2 solubility and thus more CO2 emission.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Although the abundance of methanogens in the rumen does not necessarily linearly correlate to CH4 output, the greater abundance of methanogens in the sheep rumen than in the rabbit cecum corroborates the more CH4 produced by the former than by the latter.

    “Although the abundance of methanogens in the rumen does not necessarily linearly correlate to CH4 output (Danielsson et al., 2012; Patra and Yu, 2014), the greater abundance of methanogens in the sheep rumen than in the rabbit cecum corroborates the more CH4 produced by the former than by the latter.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Danielsson et al., 2012; Patra and Yu, 2014

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

46 of 46

  • The paper relies on this without support.

    The rate and CH4 output from herbivores are primarily determined by the availability of methanogenic substrates (H2 and CO2), which are in turn determined by the rates of production and consumption.

    “Although affected by several factors, such as pH, the rate and CH4 output from herbivores are primarily determined by the availability of methanogenic substrates (i.e., H2 and CO2), which are in turn determined by the rates of production and consumption.”

  • The paper relies on this without support.

    Sheep and New Zealand White rabbits are representative models of ruminants and non-ruminant herbivores, respectively, for comparing methane output and microbiota.

    “In the present study, we tested this hypothesis using sheep as ruminants and New Zealand White (NZW) rabbits as a non-ruminant herbivore, with alfalfa hay as the only diet.”

  • The paper relies on this without support.

    The microbiological peculiarity for the different CH4 emissions by ruminants and non-ruminant herbivores is largely unknown.

    “However, the microbiological peculiarity for the different CH4 emissions by these two groups of herbivores is largely unknown.”

  • The paper relies on this without support.

    The cecum receives no saliva.

    “while cecum receives no saliva.”

  • The paper relies on this without support.

    The cecum is a tubiform tract, while the rumen is a large sac.

    “The cecum is a tubiform tract, while the rumen is a large sac.”

  • The authors state this as an assumption.

    The Eh in the present study's sheep rumen and rabbit cecum is within the previously reported ranges.

    “We did not analyze the Eh in the present study, but it should be within the above range.”

  • The paper relies on this without support.

    The sheep and rabbits used are representative species of ruminants and non-ruminants.

    “This approach allowed us to quantitatively determine and compare CH4 production by a representative species of ruminants and non-ruminants on the basis of feed intake, feed digestibility, and metabolic BW0.75.”
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.

  • Four sheep-specific archaeal OTUs are unaccounted for

    Minor

    The three stated assignments account for 26 OTUs, rather than all 30 sheep-specific archaeal OTUs described in the sentence.

    Reported 30 · recomputed 26

  • Order of the second- and third-most predominant sheep methanogen species is reversed

    Minor

    The discussion places M. millerae ahead of M. woesei, but the reported sheep-rumen percentages are 10.8% for M. millerae and 14.6% for M. woesei.

  • Common bacterial OTU categories sum to 50, not 51

    Minor

    The listed counts of common bacterial OTUs sum to 50, one fewer than the stated total of 51.

    Reported 51 · recomputed 50

3 of 3

Cites

Flagged first, then by citations

Research works printed but not linked: 7

  1. Aronesty, 2011, ea-utils: Command-line Tools for Processing Biological Sequencing Data.
  2. Cabezas Garcia, 2017, Doctoral thesis, Swedish University of Agricultural Sciences, Umeå, Methane Production in Dairy Cows.
  3. Danielsson, 2016, Doctoral thesis, Swedish University of Agricultural Sciences, Uppsala, Methane Production in Dairy Cows.
  4. Pachauri, 2014, Core Writing Team, IPCC, 2014: Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of Intergovernmental Panel on Climate Change
  5. Nakazawa, 2015, “Mogibacterium,” in, Bergey’s Manual of Systematics of Archaea and Bacteria, 1
  6. 2015, Official Methods of Analysis.
  7. 2000, SAS User’s Guide: Statistics. Version 9.2.

Cited by

Sorted by citations

Related

Authors
Mi, L., Yang, B., Hu, X., Luo, Y., Liu, J., Yu, Z., & Wang, J.
Affiliations
  • The Ohio State University (US)
  • Zhejiang University (CN)
Corresponding author
  • Yu, Zhongtang
  • Wang, Jiakun
ORCID
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2018-03-27
Volume
9
Pages
575-575
ISSN
1664-302X (ISSN-L)
DOI
10.3389/fmicb.2018.00575
PMC
PMC5890152
OpenAlex
W2795331418
Semantic Scholar
0104d6f2935682a87ece405c723ee19b37fb5fcf
Cited by
50
References
62
Citations by year
2026: 6 · 2025: 1 · 2024: 6 · 2023: 8 · 2022: 8 · 2021: 6 · 2020: 9 · 2019: 5 · 2018: 1
FWCI
8.14
Type
journal article
Language
en
Open access
Licence
Locations
  • Frontiers in Microbiology (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Greater South Information System
Funders
  • National Natural Science Foundation of China (31372337)
  • Zhejiang University
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
rumen microbiota, cecal microbiota, sheep, rabbits, acetogenic bacteria, Butyrivibrio, Mogibacterium, Prevotella, Christensenellaceae, Bacteroides, Blautia, Ruminococcaceae, acetate to propionate ratio, rumen pH, 16S rRNA gene amplicon sequencing

About these checks

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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-26.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-26.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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