A reader asked about heart burn / excessive acid stomach / acid reflux / reflux esophagitis. This is a common symptom for a subset of CFS patients.
- “Dysbiosis, consisting of enrichment in some Gram-negative taxa (including Veillonella, Prevotella, Haemophilus, Neisseria, Campylobacter, and Fusobacterium), has been reported in association with gastroesophageal reflux disease” 
- “the study found Veillonella(19%), Prevotella (12%), Neisseria (4%), and Fusobacterium (9%) to be more prevalent in patients with reflux esophagitis and Barrett’s esophagus than in controls.” 
- “Notably, increased levels of Enterobacteriaceae were observed in the gastric fluid of oesophagitis and BE patients.” 
- “The advent of widespread antibiotic use occurred in the 1950s, preceding the surge of EA.” 
Proton Pump Inhibitors
- Common treatment like Proton Pump inhibitors “change the populations of microbes living in the intestines … PPI use makes some infections 1.5 times as likely, ” [2015 Medscape]
- The BMJ article had a nice graphic of what PPI’s do with red indicting higher growth and blue with decrease. For example, bifidobacteriaceae is decreased (and it was already low in CFS patients), lactobacillales is increased (increase the level of D-lactic acidosis).
- “increased Enterococcaceae and Streptococcaceae, decreased Clostridiales…increased Micrococcaceae and Staphylococcaceae …an increase in genes involved in bacterial invasion.”
Possible Herb Treatments
Enterobacteriaceae is increased, but the increase appear to be for specific species. I went thru all of the above overgrowth and found a few items that appear to reduce some of them.
- Magnolia officinalis  
- Olive oil 
- Luteolin  “Dietary sources include celery, broccoli, green pepper, parsley, thyme, dandelion, perilla, chamomile tea, carrots, olive oil, peppermint, rosemary, navel oranges, and oregano” [wikipedia]
- Radix Bupleuri 
- “Yerba Mate extracts supported and increased the growth of Lactobacillus and Pediococcus and were antimicrobial against Salmonella and Campylobacter” 
Possible Probiotic Treatments
- Bifidobacterium animalis subsp lactis (B. lactis)… lower proportions of Veillonella parvula, Capnocytophaga sputigena, Eikenella corrodens, Prevotella intermedia-like species 
- “Intake of approximately one billion live B. bifidum cells affected the relative abundance… specifically, Prevotellaceae (P = 0.041) and Prevotella (P = 0.034) were significantly decreased, whereas Ruminococcaceae (P = 0.039) and Rikenellaceae (P = 0.010) were significantly increased.” 
- BUT NOT: “L. rhamnosus GG [Culturelle] supplementation has an influence on the composition of the intestinal microbiota in children, causing an increase in the abundance of Prevotella,”
- “L. gasseri inhibition of [Neisseria] gonococcal adherence is a multifactorial process” 
- “Lactobacillus curvatus DN317 [very specific strain] .. found to be bacteriostatic against Campylobacter jejuni ATCC 33560.”
- BUT NOT: “L. reuteri intake correlated with increased S. oralis/S. mitis/S. mitis bv2/S. infantis group and Campylobacter concisus, Granulicatella adiacens, Bergeyella sp. HOT322, Neisseria subflava, and SR1 [G-1] sp. HOT874 detection and reduced S. mutans, S. anginosus, N. mucosa, Fusobacterium periodicum, F. nucleatum ss vincentii, and Prevotella maculosa detection. This effect had disappeared 1 month after exposure was terminated.”  — unclear if it will help or hurt
It appears that reflux esophagitis is caused by a bacteria shift. It was surprising to find zero studies on PubMed using probiotics to treat this condition.
IMHO, yogurt is more likely to contribute to this condition than improve it.