Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy

From BugSigDB
Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-7
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Rattanathammethee T, Tuitemwong P, Thiennimitr P, Sarichai P, Na Pombejra S, Piriyakhuntorn P, Hantrakool S, Chai-Adisaksopha C, Rattarittamrong E, Tantiworawit A, Norasetthada L
Journal
PloS one
Year
2020
The intestinal bacterial flora of febrile neutropenic patients has been found to be significantly diverse. However, there are few reports of alterations of in adult acute myeloid leukemia (AML) patients. Stool samples of each treatment-naïve AML patient were collected the day before initiation of induction chemotherapy (pretreatment), on the first date of neutropenic fever and first date of bone marrow recovery. Bacterial DNA was extracted from stool samples and bacterial 16s ribosomal RNA genes were sequenced by next-generation sequencing. Relative abundance, overall richness, Shannon's diversity index and Simpson's diversity index were calculated. No antimicrobial prophylaxis was in placed in all participants. Ten cases of AML patients (4 male and 6 female) were included with a median age of 39 years (range: 19-49) and all of patients developed febrile neutropenia. Firmicutes dominated during the period of neutropenic fever, subsequently declining after bone marrow recovery a pattern in contrast to that shown by Bacteroidetes and Proteobacteria. Enterococcus was more abundant in the febrile neutropenia period compared to pretreatment (mean difference +20.2; p < 0.0001) while Escherichia notably declined during the same period (mean difference -11.2; p = 0.0064). At the operational taxonomic unit (OTU) level, there was a significantly higher level of overall richness in the pretreatment period than in the febrile neutropenic episode (mean OTU of 203.1 vs. 131.7; p = 0.012). Both of the diversity indexes of Shannon and Simpson showed a significant decrease during the febrile neutropenic period. Adult AML patients with a first episode of febrile neutropenia after initial intensive chemotherapy demonstrated a significant decrease in gut microbiota diversity and the level of diversity remained constant despite recovery of bone marrow.

Experiment 1


Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8

Curated date: 2023/03/13

Curator: Cyberian

Revision editor(s): Cyberian, Chloe, Aiyshaaaa

Subjects

Location of subjects
Thailand
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
acute myeloid leukemia acute granulocytic leukemia,acute myeloblastic leukemia,acute myelocytic leukemia,acute myelogenous leukemia,acute myelogenous leukemias,acute myeloid leukemia,acute myeloid leukemia (AML),acute non lymphoblastic leukemia,acute Nonlymphocytic leukemia,acute nonlymphocytic leukemia,AML,AML - acute myeloid leukemia,ANLL,hematopoeitic - acute Myleogenous leukemia (AML),leukemia, acute myelogenous,leukemia, acute myeloid,leukemia, acute myeloid, susceptibility to,leukemia, myelocytic, acute,myeloid leukemia, acute
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pretreatment
Group 1 name Corresponds to the case (exposed) group for case-control studies
Febrile neutropenia
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients with neutropenic fever during intensive chemotherapy
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
10
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2023/03/14

Curator: Cyberian

Revision editor(s): Cyberian, Chloe, Aiyshaaaa

Source: S1 table.

Description: The taxa that increased in relative abundance from pretreatment to febrile neutropenia.

Abundance in Group 1: increased abundance in Febrile neutropenia

NCBI Quality ControlLinks
Escherichia
Enterococcus

Revision editor(s): Cyberian, Chloe, Aiyshaaaa

Signature 2

Needs review

Curated date: 2023/03/14

Curator: Cyberian

Revision editor(s): Cyberian, Chloe

Source: S1 table.

Description: Taxa that decreased in relative abundance from pretreatment to febrile neutropenia

Abundance in Group 1: decreased abundance in Febrile neutropenia

NCBI Quality ControlLinks
Bacteroides
Sutterella

Revision editor(s): Cyberian, Chloe

Experiment 2


Needs review

Curated date: 2023/03/13

Curator: Cyberian

Revision editor(s): Cyberian, Aiyshaaaa

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
febrile neutropenia
Group 1 name Corresponds to the case (exposed) group for case-control studies
Bone marrow recovery
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
After initiation of induction chemotherapy

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2023/03/25

Curator: Cyberian

Revision editor(s): Cyberian

Source: S1 table.

Description: The taxa that increased in relative abundance from febrile neutropenia to bone marrow recovery

Abundance in Group 1: increased abundance in Bone marrow recovery

NCBI Quality ControlLinks
Enterococcus
Streptococcus
Blautia
Veillonella
Parabacteroides

Revision editor(s): Cyberian

Signature 2

Needs review

Curated date: 2023/03/25

Curator: Cyberian

Revision editor(s): Cyberian

Source: S1 table.

Description: The taxa that decreased in relative abundance from febrile neutropenia to bone marrow recovery

Abundance in Group 1: decreased abundance in Bone marrow recovery

NCBI Quality ControlLinks
Bacteroides
Escherichia

Revision editor(s): Cyberian

Experiment 3


Needs review

Curated date: 2023/03/25

Curator: Cyberian

Revision editor(s): Cyberian, Aiyshaaaa

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-treatment
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
After initiation of induction chemotherapy treatment

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V5

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2023/03/25

Curator: Cyberian

Revision editor(s): Cyberian

Source: S1 table.

Description: taxa that increased in relative abundance from pretreatment to bone marrow recovery.

Abundance in Group 1: increased abundance in Bone marrow recovery

NCBI Quality ControlLinks
Enterococcus
Streptococcus

Revision editor(s): Cyberian

Signature 2

Needs review

Curated date: 2023/03/25

Curator: Cyberian

Revision editor(s): Cyberian

Source: S1 table.

Description: The taxa that decreased in relative abundance from pretreatment to bone marrow recovery

Abundance in Group 1: decreased abundance in Bone marrow recovery

NCBI Quality ControlLinks
Bacteroides
Blautia
Veillonella

Revision editor(s): Cyberian