Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

A Regueira‐Iglesias, C Balsa‐Castro… - Molecular Oral …, 2023 - Wiley Online Library
The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from
different works has gained particular relevance in the literature in recent years. The large …

Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies

X Yi, H Lu, X Liu, J He, B Li, Z Wang… - Microbial …, 2024 - Wiley Online Library
The human microbiome plays a crucial role in maintaining health, with advances in high‐
throughput sequencing technology and reduced sequencing costs triggering a surge in …

Waste not, want not: revisiting the analysis that called into question the practice of rarefaction

PD Schloss - Msphere, 2024 - journals.asm.org
ABSTRACT In 2014, McMurdie and Holmes published the provocatively titled “Waste not,
want not: why rarefying microbiome data is inadmissible.” The claims of their study have …

Evolving understanding of rumen methanogen ecophysiology

BH Khairunisa, C Heryakusuma, K Ike… - Frontiers in …, 2023 - frontiersin.org
Production of methane by methanogenic archaea, or methanogens, in the rumen of
ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty …

[HTML][HTML] The application of metagenomics to study microbial communities and develop desirable traits in fermented foods

M Srinivas, O O'Sullivan, PD Cotter, D Sinderen… - Foods, 2022 - mdpi.com
The microbial communities present within fermented foods are diverse and dynamic,
producing a variety of metabolites responsible for the fermentation processes, imparting …

Reproductive microbiomes in domestic livestock: insights utilizing 16S rRNA gene amplicon community sequencing

RK Poole, DR Soffa, BE McAnally, MS Smith… - Animals, 2023 - mdpi.com
Simple Summary The reproductive microbiome includes bacterial colonies within the
vagina, uterus, placental tissues and fluids, semen, and milk. Assessments of the human …

[HTML][HTML] Gut microbiome studies in livestock: achievements, challenges, and perspectives

G Forcina, L Pérez-Pardal, J Carvalheira… - Animals, 2022 - mdpi.com
Simple Summary The relentless capacity of sequencing every bit of DNA at low cost has
been fueling major advances in several research areas. This also applies to the animal …

Nanopore sequencing using the full-length 16S rRNA gene for detection of blood-borne bacteria in dogs reveals a novel species of hemotropic mycoplasma

LG Huggins, V Colella, U Atapattu… - Microbiology …, 2022 - journals.asm.org
Dogs across the globe are afflicted by diverse blood-and vector-borne bacteria (VBB), many
of which cause severe disease and can be fatal. Diagnosis of VBB infections can be …

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

L Combrink, IR Humphreys, Q Washburn… - Frontiers in …, 2023 - frontiersin.org
Extensive research in well-studied animal models underscores the importance of
commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been …

Understanding rumen microbiology: an overview

HG Perez, CK Stevenson, JM Lourenco, TR Callaway - Encyclopedia, 2024 - mdpi.com
Definition The rumen is the largest of the four chambers of the “stomach” in ruminant
animals, which harbors an incredibly dense, diverse, and dynamic microbial community …