Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

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Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Evolutionary Bioinformatics ◽

10.1177/1176934321996353 ◽

2021 ◽

Vol 17 ◽

pp. 117693432199635

Author(s):

Daoxin Liu ◽

Pengfei Song ◽

Jingyan Yan ◽

Haijing Wang ◽

Zhenyuan Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Diversity Analysis ◽

Bacterial Phyla ◽

In Captivity ◽

Relative Abundances ◽

Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

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Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis)

BioMed Research International ◽

10.1155/2021/6667715 ◽

2021 ◽

Vol 2021 ◽

pp. 1-17

Author(s):

Lijuan Yao ◽

Xiang Li ◽

Zutao Zhou ◽

Deshi Shi ◽

Zili Li ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Developmental Stages ◽

Rrna Gene ◽

Rhinopithecus Roxellana ◽

Fecal Samples ◽

Group 3 ◽

Group 2 ◽

Diverse Groups

The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.

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Changes In The Gut Microbiota After Hepatitis C Virus Eradication

10.21203/rs.3.rs-609634/v1 ◽

2021 ◽

Author(s):

Takashi Honda ◽

Masatoshi Ishigami ◽

Kenta Yamamoto ◽

Tomoaki Takeyama ◽

Takanori Ito ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Gut Microbiota ◽

Illumina Miseq ◽

Rrna Gene ◽

Virus Eradication ◽

Sequencing Platform ◽

Direct Acting Antiviral ◽

Faecal Samples ◽

Before And After

Abstract The gut microbiota interacts with infectious diseases and affects host immunity. It has also been reported that liver disease is associated with changes in the gut microbiota. To investigate changes in the gut microbiota before and after eradication of hepatitis C virus (HCV) by direct-acting antiviral (DAA) treatment in patients with chronic hepatitis C (CHC), we investigated 42 samples from 14 CHC patients who received DAA therapy for HCV. Faecal samples were obtained before treatment (Pre), when treatment ended (EOT), and 24 weeks after treatment ended (Post24). The target V3–4 region of the 16S rRNA gene from faecal samples was amplified using the Illumina Miseq sequencing platform. The diversity of the gut microbiota did not differ significantly between Pre, EOT, and Post24. PCoA analysis showed that for each patient, the values at Pre, EOT, and Post 24 were concentrated within a small area. LEfSe analysis showed that the relative abundances of Faecalibacterium and Bacillus were increased at EOT and further increased at Post24, and these genera were significantly increased at Post24 compared to Pre. These results suggest that changes in the gut microbiota need to be considered as among the various effects on living organisms observed after HCV elimination.

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A Metagenomic Analysis of the Equine Gut Microbiome with and Without Probiotic Supplementation (P09-006-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz033.p09-006-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Olivia Konen ◽

Kristin Peters ◽

Petra Tsuji

Keyword(s):

Relative Abundance ◽

Illumina Miseq ◽

Experimental Manipulation ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Probiotic Supplementation ◽

Fecal Matter ◽

Microbiome Composition ◽

Bacterial Phyla ◽

And Mathematics

Abstract Objectives The goal of this study is to compare the microbiome of domesticated horses with and without probiotic supplementation. Methods Our University's Institutional Animal Care and Use Committee has granted an exemption, as the horses were not housed on campus and there was no experimental manipulation to the horses’ feeding implemented. Fecal matter from six privately owned horses maintained on their standard grazing diet were collected. Three of the six horses received a probiotic supplement, SmartDigest, for several years prior to beginning the project. Supplementation ceased for one month, and samples were again obtained. The other three horses never received probiotics. Bacterial DNA was isolated from all fecal samples, the 16S rRNA gene amplified, tagged with index primers, and subsequently sequenced using the Illumina MiSeq. Results Dominant groups from non-supplemented horses residing on the same property included the phyla bacteriodetes, firmicutes, proteobacteria, and verrucomicrobia. Interestingly, Sphingobacterium bambusae was identified in all three horses, even though this species has previously been isolated from the soil of bamboo plantations. Currently, samples from horses with probiotics are being analyzed. We are also employing qPCR analysis to validate the NextGen data, and to further investigate relative abundance of specific bacterial groups relevant to equine intestinal health. Conclusions Preliminary NextGen sequence analysis of the relative abundance of bacterial phyla suggests that, as expected, the horses residing on the same property and thus receiving the same diet possess a similar intestinal microbiome composition. Similarities between horses persist down to the genus level, and are now being compared to samples from horses on a probiotic-supplemented diet. Funding Sources Financial support was provided by Towson University's Fisher College of Science and Mathematics, and Jess and Mildred Fisher Endowed Chair funds to P. Tsuji.

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PSII-24 Towards a better understanding of the gut microbiome functions in the swine production: extensive cultivation of the swine gut microbiome from different growth stages

Journal of Animal Science ◽

10.1093/jas/skz258.493 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 242-243

Author(s):

Xiaofan Wang ◽

Xiaoyuan Wei ◽

Feilong Deng ◽

Tsungcheng Tsai ◽

Charles V Maxwell ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Pathogenic Bacteria ◽

Illumina Miseq ◽

Positive Control ◽

Growth Stages ◽

Rrna Gene ◽

Swine Production ◽

Fecal Samples ◽

Different Growth Stages

Abstract Substantial progress has been made in the culture-omics of the human gut microbiota. However, little is known about the culture-omics of the swine gut microbiota, despite recent reports of their significant roles in swine health and production. To fill this knowledge gap in research, we tested 52 bacterial cultivation methods with different media and gas combinations. Fresh fecal samples (0.2g/sample) were collected from three pigs at the end of four growth stages: lactation, nursery, growing and finishing and were mixed with a stomacher in 20 mL saline. Aliquots of 50 uL microbial suspensions were then spread onto different media plates and incubated under aerobic and anaerobic conditions at 37C for up to 5 days. An additional aliquot of each sample was subjected to direct DNA extraction as a positive control. Bacterial colonies from each plate were collected and DNA was extracted from these samples using the Powersoil DNA isolation kit and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 378, 482, 565, and 555 bacterial features were observed from microbial solutions at the end of lactation, nursery, growing and finishing. Our culturing methods recovered 415, 675, 808, and 823 features correspondingly, representing 45.2%, 54.8%, 53.3%, and 56.4% of total features observed in microbial solutions. The top ten most easily cultured genus were Escherichia, Streptococcus, Lactobacillus, Megasphaera, Acidaminococcus, Bacillus, Mitsuokella, Enterococcus and Prevotella. Non-parametric permutational multivariate analysis of variance shows that the main factors driving the swine culture-omics included medium, age and oxygen condition. This study identifies the cultivable bacteria from fecal samples collected at different growth stages of pigs and provides a guidance to cultivate potential beneficial or pathogenic bacteria of interests and validate their functions in swine production.

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Production of conjugated linoleic acid (CLA): effect of inulin on microbial composition and CLA concentration in a human intestinal model

Proceedings of The Nutrition Society ◽

10.1017/s0029665120005777 ◽

2020 ◽

Vol 79 (OCE2) ◽

Author(s):

Ilaria Carafa ◽

Domenico Masuero ◽

Urska Vrhovsek ◽

Giovanni Bittante ◽

Elena Franciosi ◽

...

Keyword(s):

Linoleic Acid ◽

Gut Microbiota ◽

Relative Abundance ◽

Illumina Miseq ◽

Ultra Performance Liquid Chromatography ◽

Rrna Gene ◽

Human Gut ◽

Microbial Composition ◽

Human Gut Microbiota

AbstractConjugated linoleic acids (CLAs) show a number of putative health-promoting activities including anti-carcinogenic, anti-adipogenic, anti-diabetogenic, anti-inflammatory and antioxidant actions. CLAs are naturally produced by ruminal bacteria and several studies demonstrate that various lactobacilli and bifidobacteria are also able to produce CLAs in vitro from linoleic acid (LA). However, the ability of the human gut microbiota to produce CLA is less extensively studied. Our hypothesis is that the human gut microbiota is able to convert LA to CLA, and that the readily fermentable fiber inulin would positively modulate the growth of CLA-producing bacteria and, consequently increase the CLA content in the intestine.The capability of the faecal microbiota from five healthy donors to produce CLA was tested in anaerobic batch cultures for 48 hours at pH 5.5 and 6.5. Test treatments were linoleic acid (LA; 1 mg/mL) + bovine serum albumin (BSA; 0.2 mg/mL), and LA (1 mg/mL) + BSA (0.2 mg/mL) + inulin (1%, w/v) compared to a control BSA (0.2 mg/mL) fermentation. The microbial composition was analyzed 0, 24 and 48 hours after starting the fermentation by 16S rRNA gene Illumina MiSeq sequencing (V3-V4 region). CLAs were quantified by Ultra performance liquid chromatography - tandem mass spectrometer (UPLC-MS/MS) and bi-dimensional gas chromatography (GC x GC).The inclusion of LA + BSA + inulin at pH 5.5 significantly increased the relative abundance of Collinsella aerofaciens (p < 0.05), and tended to increase the relative abundance of bifidobacteria. LA + BSA + inulin at both pH 5.5 and 6.5 reduced the relative abundance of Parabacteroides, Bilophila, Clostridia and Enterobacteriaceae (p < 0.05). The concentration of CLA, in particular the isomer cis9,trans11 C18:2, was significantly higher in the LA + BSA + inulin group at pH 5.5 after 24 and 48 hours fermentation.The data show that the treatment LA + BSA + inulin at pH 5.5 induce substantial changes in microbiota composition, including bifidogenesis and CLA production in a human intestinal microbiota model. The changes of relative abundance detected are consistent with changes in gut bacteria previously linked to human health. Collinsella aerofaciens has been reported for reducing bloating, in particular in subjects suffering from irritable bowel syndrome, while Clostridia, Bilophila and Enterobacteriaceae causes human infections. In addition, the increase of bifidobacteria and LAB, which have previously been shown in vitro to produce CLA, may also be involved in CLA production under simulated cecal microbiome. These preclinical observations warrant confirmation in suitably designed animal and human mechanistic studies.

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Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Gut Pathogens ◽

10.1186/s13099-019-0341-6 ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 20

Author(s):

Mohammad Tauqeer Alam ◽

Gregory C. A. Amos ◽

Andrew R. J. Murphy ◽

Simon Murch ◽

Elizabeth M. H. Wellington ◽

...

Keyword(s):

Inflammatory Bowel Disease ◽

Gut Microbiota ◽

Bowel Disease ◽

Gut Microbiome ◽

Global Scale ◽

Rrna Gene ◽

Healthy Individuals ◽

Bacterial Phyla ◽

Inflammatory Bowel ◽

Bacterial Groups

Abstract Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.

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Maternal group B Streptococcus and the infant gut microbiota

Journal of Developmental Origins of Health and Disease ◽

10.1017/s2040174415001361 ◽

2015 ◽

Vol 7 (1) ◽

pp. 45-53 ◽

Cited By ~ 16

Author(s):

A. E. Cassidy-Bushrow ◽

A. Sitarik ◽

A. M. Levin ◽

S. V. Lynch ◽

S. Havstad ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Negative Binomial ◽

Group B Streptococcus ◽

Illumina Miseq ◽

Rrna Gene ◽

Adult Disease ◽

Gut Colonization ◽

Infant Gut Microbiome ◽

Group B

Early patterns of gut colonization may predispose children to adult disease. Exposures in utero and during delivery are associated with the infant gut microbiome. Although ~35% of women carry group B strep (GBS; Streptococcus agalactiae) during pregnancy, it is unknown if GBS presence influences the infant gut microbiome. As part of a population-based, general risk birth cohort, stool specimens were collected from infant’s diapers at research visits conducted at ~1 and 6 months of age. Using the Illumina MiSeq (San Diego, CA) platform, the V4 region of the bacterial 16S rRNA gene was sequenced. Infant gut bacterial community compositional differences by maternal GBS status were evaluated using permutational multivariate analysis of variance. Individual operational taxonomic units (OTUs) were tested using a zero-inflated negative binomial model. Data on maternal GBS and infant gut microbiota from either 1 (n=112) or 6-month-old stool (n=150) specimens was available on 262 maternal-child pairs. Eighty women (30.5%) were GBS+, of who 58 (72.5%) were given intrapartum antibiotics. After adjusting for maternal race, prenatal antifungal use and intrapartum antibiotics, maternal GBS status was statistically significantly associated with gut bacterial composition in the 6 month visit specimen (Canberra R2=0.008, P=0.008; Unweighted UniFrac R2=0.010, P=0.011). Individual OTU tests revealed that infants of GBS+ mothers were significantly enriched for specific members of the Clostridiaceae, Ruminococcoceae, and Enterococcaceae in the 6 month specimens compared with infants of GBS- mothers. Whether these taxonomic differences in infant gut microbiota at 6 months lead to differential predisposition for adult disease requires additional study.

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Effects of Clostridium butyricum on growth performance, metabonomics and intestinal microbial differences of weaned piglets

BMC Microbiology ◽

10.1186/s12866-021-02143-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jing Liang ◽

Shasha Kou ◽

Cheng Chen ◽

Sayed Haidar Abbas Raza ◽

Sihu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Growth Performance ◽

Intestinal Microbiota ◽

Relative Abundance ◽

Statistical Significance ◽

Clostridium Butyricum ◽

Rrna Gene ◽

Gut Health ◽

Weaned Piglets ◽

Bacterial Phyla

Abstract Background Weaning stress of piglets causes a huge economic loss to the pig industry. Balance and stability of the intestinal microenvironment is an effective way to reduce the occurance of stress during the weaning process. Clostridium butyricum, as a new microecological preparation, is resistant to high temperature, acid, bile salts and some antibiotics. The aim of present study is to investigate the effects of C. butyricum on the intestinal microbiota and their metabolites in weaned piglets. Results There was no statistical significance in the growth performance and the incidence of diarrhoea among the weaned piglets treated with C. butyricum during 0–21 days experimental period. Analysis of 16S rRNA gene sequencing results showed that the operational taxonomic units (OTUs), abundance-based coverage estimator (ACE) and Chao index of the CB group were found to be significantly increased compared with the NC group (P < 0.05). Bacteroidetes, Firmicutes and Tenericutes were the predominant bacterial phyla in the weaned piglets. A marked increase in the relative abundance of Megasphaera, Ruminococcaceae_NK4A214_group and Prevotellaceae_UCG-003, along with a decreased relative abundance of Ruminococcaceae_UCG-005 was observed in the CB group, when compared with the NC group (P < 0.05). With the addition of C. butyricum, a total of twenty-two significantly altered metabolites were obtained in the feces of piglets. The integrated pathway analysis by MetaboAnalyst indicated that arginine and proline metabolism; valine, leucine and isoleucine biosynthesis; and phenylalanine metabolism were the main three altered pathways, based on the topology. Furthermore, Spearman’s analysis revealed some altered gut microbiota genus such as Oscillospira, Ruminococcaceae_NK4A214_group, Megasphaera, Ruminococcaceae_UCG-005, Prevotella_2, Ruminococcaceae_UCG-002, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-003 were associated with the alterations in the fecal metabolites (P < 0.05), indicating that C. butyricum presented a potential protective impact through gut microbiota. The intestinal metabolites changed by C. butyricum mainly involved the variation of citrulline, dicarboxylic acids, branched-chain amino acid and tryptophan metabolic pathways. Conclusions Overall, this study strengthens the idea that the dietary C. butyricum treatment can significantly alter the intestinal microbiota and metabolite profiles of the weaned piglets, and C. butyricum can offer potential benefits for the gut health.

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Host Phylogeny Determines The Gut Microbial Landscape of Cephalopods

10.21203/rs.3.rs-556214/v2 ◽

2021 ◽

Author(s):

Woorim Kang ◽

Pil Soo Kim ◽

Euon Jung Tak ◽

Hojun Sung ◽

Na-Ri Shin ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Gut Microbiome ◽

Circulatory System ◽

Illumina Miseq ◽

Phylogenetic Position ◽

Rrna Gene ◽

Microbial Composition ◽

Host Phylogeny ◽

Gut Microbial Community

Abstract BackgroundCompared to vertebrate gut microbiomes, little is known about the factors shaping the gut microbiomes in invertebrates, especially in non-insect invertebrates. Class Cephalopoda is the only group in the phylum Mollusca characterized by a closed circulatory system and a well-differentiated digestive system to process their carnivorous diet. Despite their key phylogenetic position for comparative studies as well as their ecological and commercial importances, analyses of the cephalopod gut microbiome are limited. In this study, we characterized the gut microbiota of six species of wild cephalopods by Illumina MiSeq sequencing of 16S rRNA gene amplicons.ResultsEach cephalopod gut consisted of a distinct consortium of microbes. Photobacterium and Mycoplasma were prevalent in all cephalopod hosts and were identified as core taxa. The gut microbial composition reflected host phylogeny. The importance of host phylogeny was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma, although Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Further, we showed that class Cephalopoda has a distinct gut microbial community from those of other molluscan groups. The gut microbiota of the phylum Mollusca was determined by host phylogeny, diet, and environment (aquatic vs. terrestrial).ConclusionWe provide the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of the distinctive microbes and strongly associated with their phylogeny. The genera Photobacterium and Mycoplasma are core taxa in the cephalopod gut microbiota. Collectively, our findings of this study provide evidence that cephalopod and mollusk gut microbiomes reflect phylogeny, environment, and the diet of the host and these data can be suggested to establish future directions for invertebrate gut microbiome research.

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